Anti-pathogen treatments

ABSTRACT

Chimeric molecules that contain at least one pathogen-detection domain and at least one effector domain, and their methods of use in preventing or treating a pathogen infection in a cell or organism are described. The pathogen-detection domain and effector domain of the chimeric molecules are domains not typically found in nature to be associated together. Agents are also described herein having at least one pathogen-interacting molecular structure and at least one effector-mediating molecular structure, the agent being one that is non-naturally-occurring in a cell. The methods of prevention and treatment described herein are effective for a broad spectrum of pathogens and exhibit little or no toxic side-effects. Assays for the detection of a pathogen, pathogen component, or product produced or induced by a pathogen, are also provided.

RELATED APPLICATIONS

This application is a Divisional of U.S. application Ser. No.10/361,208, filed on Feb. 7, 2003, which claims the benefit of U.S.Provisional Application No. 60/355,359, filed Feb. 7, 2002, U.S.Provisional Application No. 60/355,022, filed Feb. 7, 2002, and U.S.Provisional Application No. 60/432,386, filed Dec. 10, 2002.

The entire teachings of the above applications are incorporated hereinby reference.

GOVERNMENT SUPPORT

The invention was supported, in whole or in part, by contract numberF19628-00-C-0002 from the United States Air Force. The Government hascertain rights in the invention.

BACKGROUND OF THE INVENTION

Many pathogens have the ability to evade the natural defenses of aninfected host cell or organism. Consequently, the infected host developsthe disease or disorder which is associated with that pathogen.

Treatments for pathogenic infections typically target a distinguishingfeature or characteristic of a specific pathogen. For example, acyclovirtargets the replication stage of herpesvirus infection, zidovudine/AZTtargets the reverse transcriptase of human immunodeficiency virus (HIV),and various protease inhibitors target HIV protease. Generally, however,these therapies have many disadvantages, including limited usefulnessfor only a specific pathogen, ineffectiveness due to pathogen variation,and toxic side effects. In addition, many of these therapies tend to beslow to develop.

A need exists therefore, for the development of anti-pathogen therapiesthat are effective for a broad spectrum of pathogens and which overcomedisadvantages of existing therapies.

SUMMARY OF THE INVENTION

The present invention relates to an agent, such as a chimeric molecule,or components thereof, which are capable of being assembled together toform said chimeric molecule or agent, as described herein. The chimericmolecule or agent of the invention has at least one pathogen-detectiondomain (or a pathogen-recognition domain), or molecular structure thatis capable of specifically interacting with a pathogen, pathogencomponent, pathogen product or pathogen-induced product, and/or at leastone effector domain, or molecular structure capable of eliciting adesired effector function, these domains or molecular structures notbeing typically associated or bound together in nature. This inventionalso relates to the use of this agent for the treatment or prevention ofa pathogen infection in a cell or an organism.

In one embodiment, a method for treating or preventing a pathogeninfection in a cell includes administering to a cell chimeric moleculeshaving at least one pathogen-detection domain and at least one effectordomain, such pathogen-detection domain and effector domain being notnormally bound to each other, and wherein in the presence of a pathogenin the cell, the chimeric molecules bind to the pathogen, pathogencomponent or pathogen product, and activate the effector domain, thustreating or preventing the pathogen infection in the cell.

In another embodiment, a method for treating or preventing a pathogeninfection in a cell includes administering to a cell chimeric moleculeshaving at least one pathogen-induced product-detection domain and atleast one effector domain, such pathogen-induced product-detectiondomain and effector domain being not normally bound to each other, andwherein in the presence of a pathogen-induced product in a cell, thechimeric molecules bind to the pathogen-induced product and activate theeffector domain, thus treating or preventing the pathogen infection inthe cell.

In a further embodiment, a method for treating or preventing the spreadof a pathogen infection in an organism, includes administering to theorganism, chimeric molecules having at least one pathogen-detectiondomain and at least one effector domain, such pathogen-detection domainand effector domain being not normally bound to each other, and whereinin the presence of a pathogen in the organism, the chimeric moleculesbind to the pathogen, pathogen component or pathogen product, andactivate the effector domain, thus treating or preventing the spread ofthe pathogen infection in the organism.

In a still further embodiment, a method for treating or preventing thespread of a pathogen infection in an organism, includes administering tothe organism, chimeric molecules having at least one pathogen-inducedproduct-detection domain and at least one effector domain, suchpathogen-induced product-detection domain and effector domain being notnormally bound to each other, and wherein in the presence of apathogen-induced product in the organism, the chimeric molecules bind tothe pathogen-induced product and activate the effector domain, thustreating or preventing the spread of the pathogen infection in theorganism.

In another embodiment of the invention, a method of treating orpreventing a pathogen infection in a cell includes administering to acell an agent having at least one pathogen-interacting molecularstructure and at least one effector-mediating molecular structure, suchpathogen-interacting molecular structure and effector-mediatingmolecular structure being a non-naturally occurring agent in a cell, andwherein in the presence of a pathogen in a cell, the agent binds to thepathogen, pathogen component or pathogen product, and activates theeffector-mediating molecular structure, thus treating or preventing thepathogen infection in the cell.

In still another embodiment of the invention, a method of treating orpreventing a pathogen infection in a cell includes administering to acell an agent having at least one pathogen-induced product-interactingmolecular structure and at least one effector-mediating molecularstructure, such pathogen-induced product-interacting molecular structureand effector-mediating molecular structure being a non-naturallyoccurring agent in a cell, and wherein in the presence of apathogen-induced product in a cell, the agent binds to thepathogen-induced product and activates the effector-mediating molecularstructure, thus treating or preventing the pathogen infection in thecell.

In a further embodiment, a method for treating or preventing the spreadof a pathogen infection in an organism, includes administering to theorganism an agent having at least one pathogen-interacting molecularstructure and at least one effector-mediating molecular structure, suchpathogen-interacting molecular structure and effector-mediatingmolecular structure being a non-naturally occurring agent in a cell, andwherein in the presence of a pathogen in the organism, the agent bindsto the pathogen, pathogen component or pathogen product, and activatesthe effector-mediating molecular structure, thus treating or preventingthe spread of the pathogen infection in the organism.

In another embodiment, a method for treating or preventing the spread ofa pathogen infection in an organism, includes administering to theorganism an agent having at least one pathogen-inducedproduct-interacting molecular structure and at least oneeffector-mediating molecular structure, such pathogen-inducedproduct-interacting molecular structure and effector-mediating molecularstructure being a non-naturally occurring agent in a cell, and whereinin the presence of a pathogen in the organism, the agent binds to thepathogen-induced product and activates the effector-mediating molecularstructure, thus treating or preventing the spread of the pathogeninfection in the organism.

In yet another embodiment of the invention, a method of treating orpreventing a pathogen infection in a cell includes administering to thecell individual components of a chimeric molecule, such components beingassembled together to form a chimeric molecule having at least onepathogen-detection domain and at least one effector domain, suchpathogen-detection domain and effector domain being not normally boundto each other, and wherein in the presence of a pathogen, pathogencomponent or pathogen product in the cell, the chimeric molecules bindto the pathogen, pathogen component or pathogen product in the cell, andactivate the effector domain, thus treating or preventing the pathogeninfection in the cell.

In another embodiment of the invention, a method of treating orpreventing a pathogen infection in a cell includes administering to thecell individual components of a chimeric molecule, such components beingassembled together to form a chimeric molecule having at least onepathogen-induced product-detection domain and at least one effectordomain, such pathogen-induced product-detection domain and effectordomain being not normally bound to each other, and wherein in thepresence of a pathogen-induced product in a cell, the chimeric moleculesbind to the pathogen-induced product and activate the effector domain,thus treating or preventing the pathogen infection in the cell.

In still another embodiment of the invention, a method of treating orpreventing a pathogen infection in an organism includes administering tothe organism individual components of a chimeric molecule, suchcomponents being assembled together to form a chimeric molecule havingat least one pathogen-detection domain and at least one effector domain,such pathogen-detection domain and effector domain being not normallybound to each other, and wherein in the presence of a pathogen in theorganism, the chimeric molecules bind to the pathogen, pathogencomponent or pathogen product, and activate the effector domain, thustreating or preventing the spread of the pathogen infection in theorganism.

In another embodiment of the invention, a method of treating orpreventing a pathogen infection in an organism includes administering tothe organism individual components of a chimeric molecule, suchcomponents being assembled together to form a chimeric molecule havingat least one pathogen-induced product-detection domain and at least oneeffector domain, such pathogen-induced product-detection domain andeffector domain being not normally bound to each other, and wherein inthe presence of a pathogen-induced product in the organism, the chimericmolecules bind to the pathogen-induced product and activate the effectordomain, thus treating or preventing the spread of the pathogen infectionin the organism.

In a further embodiment of the invention, a chimeric molecule isprovided which has at least one pathogen-detection domain and at leastone effector domain, such pathogen-detection domain and effector domainbeing one that is non-naturally-occurring in a cell.

In a still further embodiment of the invention, a chimeric molecule isprovided which has at least one pathogen-induced product-detectiondomain and at least one effector domain, such pathogen-inducedproduct-detection domain and effector domain being one that isnon-naturally-occurring in a cell.

In yet another embodiment of the invention, an agent is provided whichhas at least one pathogen-interacting molecular structure and at leastone effector-mediating molecular structure, such agent being one that isnon-naturally-occurring in a cell.

In a further embodiment of the invention, an agent is provided which hasat least one pathogen-induced product-interacting molecular structureand at least one effector-mediating molecular structure, such agentbeing one that is non-naturally-occurring in a cell.

In another embodiment of the invention, an assay for the detection of apathogen infection in a cell includes culturing the cell in a suitablecell culture medium and administering to the cell chimeric moleculeshaving at least one pathogen-detection domain and at least one effectordomain, such chimeric molecule being one that is non-naturally-occurringin a cell, wherein in the presence of a pathogen, pathogen component orpathogen product in the cell, the chimeric molecules bind to thepathogen, pathogen component or pathogen product, and activate theeffector domain, thus determining the presence or absence of apoptosisin the cell indicates the presence or absence of a pathogen infection inthe cell.

In yet another embodiment of the invention, an assay for the detectionof a pathogen infection in an organism includes obtaining a cell orcells from the organism and culturing the cell(s) in a suitable cellculture medium and administering to the cell(s) chimeric moleculeshaving at least pathogen-detection domain and at least one effectordomain, such chimeric molecule being one that is non-naturally-occurringin a cell, wherein in the presence of a pathogen, pathogen component orpathogen product, chimeric molecules bind to the pathogen, pathogencomponent or pathogen product, and activate the effector domain. Thus,determining the presence or absence of apoptosis in the cell isolatedfrom the organism indicates the presence or absence of a pathogeninfection in the organism.

In a still further embodiment of the invention, an assay for thedetection of a pathogen infection in an organism, includes obtaining asample from the organism and adding the sample to an uninfected cell,then culturing this cell in a suitable cell culture medium andadministering to that cell chimeric molecules having at least onepathogen-detection domain and at least one effector domain, suchchimeric molecules are non-naturally-occurring in a cell, wherein in thepresence of a pathogen, pathogen component or pathogen product, thechimeric molecules bind to the pathogen, pathogen component or pathogenproduct, and activate the effector domain. Thus, determining thepresence or absence of effector domain activation indicates the presenceor absence of a pathogen infection in the sample obtained from theorganism.

In a still further embodiment of the invention, an assay for thedetection of a pathogen infection in an organism, includes obtaining asample from the organism and adding the sample to an uninfected cell,then culturing this cell in a suitable cell culture medium andadministering to that cell an agent having at least onepathogen-interacting molecular structure and at least oneeffector-mediating molecular structure, such agent being one that isnon-naturally-occurring in a cell, wherein in the presence of apathogen, pathogen component or pathogen product in the cell, the agentbinds to the pathogen, pathogen component or pathogen product, andactivates the effector-mediating molecular structure. Thus, determiningthe presence or absence of activation of the effector-mediatingmolecular structure in the cell indicates the presence or absence of apathogen infection in the sample obtained from the organism.

In further embodiment of the invention, an assay for the detection of apathogen infection in a cell includes culturing the cell in a suitablecell culture medium and administering to that cell an agent having atleast one pathogen-interacting molecular structure and at least oneeffector-mediating molecular structure, such agent being one that isnon-naturally-occurring in a cell, wherein in the presence of apathogen, pathogen component or pathogen product in the cell, the agentbinds to the pathogen, pathogen component or pathogen product, andactivates the effector-mediating molecular structure. Thus, determiningthe presence or absence of activation of the effector-mediatingmolecular structure in the cell indicates the presence or absence of apathogen infection in the cell.

In another embodiment of the invention, an assay for the detection of apathogen infection in an organism includes obtaining a cell or cellsfrom the organism and culturing the cell(s) in a suitable cell culturemedium and administering to the cell(s) an agent having at least onepathogen-interacting molecular structure and at least oneeffector-mediating molecular structure, such agent being one that isnon-naturally-occurring in a cell, wherein in the presence of apathogen, pathogen component or pathogen product, chimeric moleculesbind to the pathogen, pathogen component or pathogen product, andactivate the effector-mediating molecular structure. Thus, determiningthe presence or absence of activation of the effector-mediatingmolecular structure in the cell indicates the presence or absence of apathogen infection in the organism.

In another embodiment of the invention, an assay for the detection of apathogen infection in a cell includes culturing the cell in a suitablecell culture medium and administering to the cell chimeric moleculeshaving at least one pathogen-induced product-detection domain and atleast one effector domain, such chimeric molecule being one that isnon-naturally-occurring in a cell, wherein in the presence of apathogen-induced product in the cell, the chimeric molecules bind to thepathogen-induced product, and activate the effector domain, thusdetermining the presence or absence of apoptosis in the cell indicatesthe presence or absence of a pathogen infection in the cell.

In yet another embodiment of the invention, an assay for the detectionof a pathogen infection in an organism includes obtaining a cell orcells from the organism and culturing the cell(s) in a suitable cellculture medium and administering to the cell(s) chimeric moleculeshaving at least pathogen-induced product-detection domain and at leastone effector domain, such chimeric molecule being one that isnon-naturally-occurring in a cell, wherein in the presence of apathogen, pathogen component or pathogen product, chimeric moleculesbind to the pathogen-induced product, and activate the effector domain.Thus, determining the presence or absence of apoptosis in the cellisolated from the organism indicates the presence or absence of apathogen infection in the organism.

In further embodiment of the invention, an assay for the detection of apathogen infection in a cell includes culturing the cell in a suitablecell culture medium and administering to that cell an agent having atleast one pathogen-induced product-interacting molecular structure andat least one effector-mediating molecular structure, such agent beingone that is non-naturally-occurring in a cell, wherein in the presenceof a pathogen-induced product in the cell, the agent binds to thepathogen-induced product, and activates the effector-mediating molecularstructure. Thus, determining the presence or absence of activation ofthe effector-mediating molecular structure in the cell indicates thepresence or absence of a pathogen infection in the cell.

In a still further embodiment of the invention, an assay for thedetection of a pathogen infection in an organism, includes obtaining asample from the organism and adding the sample to an uninfected cell,then culturing this cell in a suitable cell culture medium andadministering to that cell chimeric molecules having at least onepathogen-induced product-detection domain and at least one effectordomain, such chimeric molecules are non-naturally-occurring in a cell,wherein in the presence of a pathogen-induced product, the chimericmolecules bind to the pathogen-induced product, and activate theeffector domain. Thus, determining the presence or absence of effectordomain activation indicates the presence or absence of a pathogeninfection in the sample obtained from the organism.

In a still further embodiment of the invention, an assay for thedetection of a pathogen infection in an organism, includes obtaining asample from the organism and adding the sample to an uninfected cell,then culturing this cell in a suitable cell culture medium andadministering to that cell an agent having at least one pathogen-inducedproduct-interacting molecular structure and at least oneeffector-mediating molecular structure, such agent being one that isnon-naturally-occurring in a cell, wherein in the presence of apathogen-induced product, chimeric molecules bind to thepathogen-induced product, and activate the effector-mediating molecularstructure. Thus, determining the presence or absence of activation ofthe effector-mediating molecular structure in the cell indicates thepresence or absence of a pathogen infection in the sample obtained fromthe organism.

In another embodiment of the invention, an assay for the detection of apathogen infection in an organism includes obtaining a cell or cellsfrom the organism and culturing the cell(s) in a suitable cell culturemedium and administering to the cell(s) an agent having at least onepathogen-induced product-interacting molecular structure and at leastone effector-mediating molecular structure, such agent being one that isnon-naturally-occurring in a cell, wherein in the presence of apathogen-induced product, chimeric molecules bind to thepathogen-induced product, and activate the effector-mediating molecularstructure. Thus, determining the presence or absence of activation ofthe effector-mediating molecular structure in the cell indicates thepresence or absence of a pathogen infection in the organism.

In another embodiment, a method for treating or preventing the spread ofa pathogen infection in an organism, includes administering to theorganism, chimeric molecules having at least one pathogen-detectiondomain and at least one effector domain, such pathogen-detection domainand effector domain being not normally bound to each other, and whereinthe presence of a pathogen in the organism, the chimeric molecules bindto the pathogen, pathogen component or pathogen product and activate theeffector domain, thus treating or preventing the spread of the pathogeninfection in the organism.

In yet another embodiment, the method includes administering to a cellchimeric molecules which have at least one double-stranded RNA bindingdomain and at least one apoptosis mediator domain, the chimeric moleculebeing one that is non-naturally-occurring in a cell, such that in thepresence of a pathogen in the cell, chimeric molecules bind to thedouble-stranded RNA produced by the pathogen and activate the apoptosismediator domain, thereby causing apoptosis of the cell, thus treating orpreventing the pathogen infection in the cell.

In a further embodiment, the method includes administering to a cell anagent which has at least one double-stranded RNA-interacting molecularstructure and at least one apoptosis-effector mediating molecularstructure, the agent being one that is non-naturally-occurring in acell, such that in the presence of a pathogen in the cell, the agentbinds to the double-stranded RNA produced by the pathogen and activatesthe apoptosis-effector mediating molecular structure, thereby causingapoptosis of the cell, thus treating or preventing the pathogeninfection in the cell.

In another embodiment of the invention, a method for treating orpreventing a virus infection in a cell includes administering to thecell chimeric molecules that have at least one double-stranded RNAbinding domain and at least one apoptosis mediator domain, the chimericmolecule being one not naturally-occurring in a cell, such that in thepresence of a virus in the cell, the chimeric molecules bind to adouble-stranded RNA produced by the virus and activate the apoptosismediator domain, thereby causing apoptosis of the cell, thus treating orpreventing the virus infection in the cell.

In an additional embodiment of the invention, a method of treating orpreventing a pathogen infection in a cell includes administering to thecell chimeric molecules having at least one double-stranded RNA bindingdomain isolated from protein kinase R and at least one pro-enzymaticcaspase-3 domain, such that in the presence of a pathogen in the cell,these chimeric molecules bind to the double-stranded RNA produced by thepathogen and activate the pro-enzymatic caspase-3 domain thereby causingapoptosis of the cell, thus treating or preventing the pathogeninfection in the cell.

In another embodiment of the invention, a method of treating orpreventing a pathogen infection in a cell comprises administering to thecell chimeric molecules having at least one double-stranded RNA bindingdomain isolated from protein kinase R and at least one apoptosismediator domain isolated from Fas-associated protein with death domain(FADD), such that in the presence of a pathogen in the cell, thechimeric molecules bind to double-stranded RNA produced by the pathogenand activate the apoptosis mediator domain and cause apoptosis of thecell, thus treating or preventing the pathogen infection in the cell.

In still another embodiment of the invention, a method of treating orpreventing the spread of a pathogen infection in an organism, includesadministering to the organism chimeric molecules that have at least onedouble-stranded RNA binding domain and at least one apoptosis mediatordomain, the double-stranded RNA binding domain being one that is notnaturally bound to the apoptosis mediator domain, such that in thepresence of a pathogen in a cell or cells of the organism, the chimericmolecules bind to double-stranded RNA produced by the pathogen andactivate the apoptosis mediator domain, thereby causing apoptosis of thecell in the organism, thus treating or preventing the spread of thepathogen in the organism.

In yet another embodiment, a method of treating or preventing the spreadof a pathogen infection in an organism, includes administering to theorganism an agent which has at least one double-stranded RNA-interactingmolecular structure and at least one apoptosis-effector mediatingmolecular structure whereby, the agent being one that isnon-naturally-occurring in a cell, such that in the presence of apathogen in a cell or cells of the organism, the agent binds to thedouble-stranded RNA produced by the pathogen and activates theapoptosis-effector mediating molecular structure, thereby causingapoptosis of the cell in the organism, thus treating or preventing thespread of the pathogen in the organism.

In a further embodiment of the invention, a method of treating orpreventing the spread of a pathogen infection in an organism, includesadministering to the organism chimeric molecules having at least onedouble-stranded RNA binding domain isolated from protein kinase R and atleast one pro-enzymatic caspase-3 domain, such that in the presence ofthe pathogen in a cell or cells of the organism, the chimeric moleculesbind to the double-stranded RNA produced by the pathogen and activatethe pro-enzymatic caspase-3 domain, thereby causing apoptosis of thecell in the organism, thus treating or preventing the spread of thepathogen in the organism.

In another embodiment of the invention, a method for treating orpreventing the spread of a pathogen infection in an organism, includesadministering to the organism chimeric molecules that have at least onedouble-stranded RNA binding domain isolated from protein kinase R and atleast one apoptosis mediator domain isolated from FADD, such that in thepresence of the pathogen in a cell or cells of an organism, the chimericmolecules bind to double-stranded RNA produced by that pathogen andactivate the apoptosis mediator domain, thereby causing apoptosis of thecell in the organism, thus treating or preventing the spread of thepathogen in the organism.

In yet another embodiment of the invention, a method of treating orpreventing a pathogen infection in a cell includes administering to thecell individual components of a chimeric molecule, such components beingassembled together to form a chimeric molecule at least onedouble-stranded RNA binding domain and at least one apoptosis mediatordomain, such that in the presence of a pathogen in the cell, thechimeric molecules bind to double-stranded RNA produced by the pathogenand activate the apoptosis mediator domain, thus treating or preventingthe pathogen infection in the cell.

In still another embodiment of the invention, a method of treating orpreventing the spread of a pathogen infection in an organism includesadministering to the organism individual components of a chimericmolecule, such components being assembled together to form a chimericmolecule having at least one double-stranded RNA binding domain and atleast one apoptosis mediator domain, such that in the presence of apathogen, the chimeric molecules bind to double-stranded RNA produced bythe pathogen and activate the apoptosis mediator domain, thus treatingor preventing the spread of a pathogen infection in the organism.

In a further embodiment of the invention, a method of mediatingapoptosis in a cell infected with a pathogen, includes administering tothe cell chimeric molecules having at least one double-stranded RNAbinding domain and at least one apoptosis mediator domain, thedouble-stranded RNA binding domain being one that is not naturally boundto the apoptosis mediator domain, such that in the presence of apathogen in the cell, the chimeric molecules bind to the double-strandedRNA produced by that pathogen and activate the apoptosis mediatordomain, thus causing apoptosis of the cell.

In a further embodiment of the invention, a method of mediatingapoptosis in a cell infected with a pathogen, includes administering tothe cell an agent which has at least one double-stranded RNA-interactingmolecular structure and at least one apoptosis-effector mediatingmolecular structure, the agent being one that is non-naturally-occurringin a cell, such that in the presence of a pathogen, the agent binds tothe double-stranded RNA produced by the pathogen and activates theapoptosis-effector mediating molecular structure, thereby causingapoptosis of the cell.

In another embodiment of the invention, a method of mediating apoptosisin a cell infected with a pathogen, includes administering to the cellchimeric molecules having at least one double-stranded RNA bindingdomain isolated from protein kinase R and at least one pro-enzymaticcaspase-3 domain, the double-stranded RNA binding domain being one thatis not naturally bound to the apoptosis mediator domain, such that inthe presence of the pathogen in the cell, the chimeric molecules bind tothe double-stranded RNA produced by the pathogen and activatepro-enzymatic caspase-3, thus causing apoptosis of the cell.

In a further embodiment of the invention, a method of mediatingapoptosis in a cell infected with a pathogen, includes administering tothe cell chimeric molecules having at least one double-stranded RNAbinding domain isolated from protein kinase R and at least one apoptosismediator domain isolated from FADD, the double-stranded RNA bindingdomain being one that is not naturally bound to the apoptosis mediatordomain, such that in the presence of the pathogen in the cell, thechimeric molecules bind to the double-stranded RNA produced by thatpathogen and activate the apoptosis mediator domain, and cause apoptosisof the cell.

In still another embodiment of the invention, a method of mediatingapoptosis in an organism infected with a pathogen, includesadministering to the organism chimeric molecules having at least onedouble-stranded RNA binding domain and at least one apoptosis mediatordomain, the double-stranded RNA binding domain being one that is notnaturally bound to the apoptosis mediator domain, such that in thepresence of the pathogen in a cell or cells of the organism, thechimeric molecules bind to the double-stranded RNA produced by thepathogen and activate apoptosis mediator domain, thereby causingapoptosis of the cell in the organism.

In another embodiment of the invention, a method of mediating apoptosisin an organism infected with a pathogen, includes administering to theorganism an agent having at least one double-stranded RNA-interactingmolecular structure and at least one apoptosis-effector mediatingmolecular structure, the agent being one that is non-naturally-occurringin a cell, such that in the presence of the pathogen in a cell or cellsof the organism, the agent binds to the double-stranded RNA produced bythe pathogen and activates the apoptosis-effector mediating molecularstructure, thereby causing apoptosis of the cell in the organism.

In further embodiment of the invention, a method of mediating apoptosisin an organism infected with a pathogen, includes administering to theorganism chimeric molecules having at least one double-stranded RNAbinding domain isolated from protein kinase R and at least onepro-enzymatic caspase-3 domain, the double-stranded RNA binding domainbeing one that is not naturally bound to the apoptosis mediator domain,such that in the presence of a pathogen in a cell or cells of theorganism, the chimeric molecules bind to the double-stranded RNAproduced by that pathogen and activate the pro-enzymatic caspase-3domain, causing apoptosis of the cell in the organism.

Another embodiment of the invention is a method of mediating apoptosisin an organism infected with a pathogen, by administering to theorganism chimeric molecules having at least one double-stranded RNAbinding domain isolated from protein kinase R and at least one apoptosismediator domain isolated from FADD, the double-stranded RNA bindingdomain being one that is not naturally bound to the apoptosis mediatordomain, such that in the presence of a pathogen in a cell or cells ofthe organism, the chimeric molecules bind to the double-stranded RNAproduced by that pathogen and activate the apoptosis mediator domain,causing apoptosis of the cell in the organism.

In another embodiment of the invention, a chimeric molecule is providedwhich has at least one double-stranded pathogen-RNA binding domain andat least one apoptosis mediator domain.

In still another embodiment, is an agent that has at least onedouble-stranded RNA-interacting molecular structure and at least oneapoptosis-effector mediating molecular structure.

In a further embodiment, a chimeric molecule is provided that has atleast one double-stranded RNA binding domain isolated from proteinkinase R and at least one apoptosis mediator domain isolated frompro-enzymatic caspase-3, the double-stranded RNA binding domain beingone that is not naturally bound to the apoptosis mediator domain.

In another embodiment, a chimeric molecule is provided that has at leastone double-stranded RNA binding domain isolated from protein kinase Rand at least one apoptosis mediator domain isolated from FADD apoptosismediator, the double-stranded RNA binding domain being one that is notnaturally bound to the apoptosis mediator domain.

In a further embodiment of the invention, a chimeric molecule havingmore than one double-stranded RNA binding domain and at least oneapoptosis mediator domain, the double-stranded RNA binding domains beingones that are not naturally bound to the apoptosis mediator domain, isprovided.

In an alternative embodiment, a chimeric molecule of the invention hasat least one double-stranded RNA binding domain and more than oneapoptosis mediator domain, the double-stranded RNA binding domain beingone that is not naturally bound to the apoptosis mediator domains.

In further embodiment of the invention, an assay for the detection of apathogen infection in a cell includes, culturing the cell in a suitablecell culture medium and administering to that cell chimeric moleculeshaving at least one double-stranded RNA binding domain and at least oneapoptosis mediator domain, the double-stranded RNA binding domain beingone that is not naturally bound to the apoptosis mediator domain, suchthat in the presence of a pathogen in the cell, the chimeric moleculesbind to the double-stranded RNA produced by the pathogen and activatethe apoptosis mediator domain, thus determining the presence or absenceof apoptosis in the cell indicates the presence or absence of apathogenic infection in the cell.

In further embodiment of the invention, an assay for the detection of apathogen infection in a cell includes, culturing the cell in a suitablecell culture medium and administering to that cell an agent having atleast one double-stranded RNA-interacting molecular structure, and atleast one apoptosis-effector mediating molecular structure, the agentbeing one that is non-naturally occurring in a cell, such that in thepresence of a pathogen in the cell, the agent binds to thedouble-stranded RNA produced by the pathogen and activates theapoptosis-effector mediating molecular structure, thus determining thepresence or absence of apoptosis in the cell indicates the presence orabsence of a pathogenic infection in the cell.

In still a further embodiment of the invention, an assay for thedetection of double-stranded RNA in a sample includes the steps ofadministering to the sample chimeric molecules having at least onedouble-stranded RNA binding domain and at least one apoptosis mediatordomain, the double-stranded RNA binding domain being one that is notnaturally bound to the apoptosis mediator domain, such that in thepresence of double-stranded RNA in the sample, the chimeric moleculeswill bind to that double-stranded RNA and activate the apoptosismediator domain. A determination of the presence or absence ofactivation of the apoptosis mediator domain will indicate the presenceor absence of double-stranded RNA in the sample.

In another embodiment of the invention, an assay for the detection ofdouble-stranded RNA in a sample includes the steps of administering tothe sample an agent having at least one double-stranded RNA-interactingmolecular structure and at least one apoptosis-effector mediatingmolecular structure, the agent being one that is non-naturally occurringin a cell, such that in the presence of double-stranded RNA in thesample, the agent binds to that double-stranded RNA and activates theapoptosis-effector mediating molecular structure, thus a determinationof the presence or absence of activation of the apoptosis-effectormediating molecular structure will indicate the presence or absence ofdouble-stranded RNA in the sample.

In further embodiment of the invention, an assay for the detection of apathogen infection in an organism includes, obtaining a cell or cellsfrom the organism, culturing the cell(s) in a suitable cell culturemedium, and administering to the cell(s) chimeric molecules having atleast one double-stranded RNA binding domain and at least one apoptosismediator domain, the double-stranded RNA binding domain being one thatis not naturally bound to the apoptosis mediator domain, such that inthe presence of a pathogen in the cell, the chimeric molecules bind tothe double-stranded RNA produced by the pathogen and activate theapoptosis mediator domain. Determining the presence or absence ofapoptosis in the cell indicates the presence or absence of a pathogenicinfection in the organism.

In another embodiment of the invention, an assay for the detection of apathogen infection in an organism includes, obtaining a cell or cellsfrom the organism, culturing the cell(s) in a suitable cell culturemedium and administering to the cell(s) an agent having at least onedouble-stranded RNA-interacting molecular structure, and at least oneapoptosis-effector mediating molecular structure, the agent being onethat is non-naturally occurring in a cell, such that in the presence ofa pathogen in the cell, the agent binds to the double-stranded RNAproduced by the pathogen and activates the apoptosis-effector mediatingmolecular structure. Determining the presence or absence of apoptosis inthe cell indicates the presence or absence of a pathogenic infection inthe organism.

The invention described herein provides chimeric molecules, and methodsof use of said chimeric molecules, for treatment and prevention ofpathogenic infections in a cell or an organism. Advantages of theclaimed invention include, for example, its applicability to a broadspectrum of pathogenic infections, in addition to its use in bothprophylactic methods and post-infection treatments. Furthermore, theclaimed invention can overcome at least some disadvantages of existingtherapies.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a chart illustrating some of the possible cellular methods fordetecting and responding (by mediating one or more effects or effectorfunctions) to pathogens. Detection methods include, but are not limitedto, detection of interferon, double-stranded RNA (dsRNA),lipopolysaccharide (LPS), and apoptosis signals. Cellular responses withanti-pathogen effects (effector functions) include, but are not limitedto, various responses from the interferon pathway, apoptosis, heatshock, and other stress responses, enhancing or inducing the immuneresponse by upregulating MHC Class I molecules on cell surfaces or byother methods, dsRNase activity, inhibition of endosome function, andnuclear localization signal inhibitors.

FIG. 2 is a simplified diagram showing three of the natural cellularpathways that interact with viruses or other pathogens. As shown, a lineending in an arrow indicates a general tendency to stimulate, while aline ending in a bar indicates a general tendency to inhibit.

FIG. 3 is a simplified diagram depicting the interferon pathway and themethods by which some pathogens inhibit it. As shown, a line ending inan arrow indicates a general tendency to stimulate, while a line endingin a bar indicates a general tendency to inhibit.

FIG. 4 is a simplified diagram showing the apoptosis pathway and themethods by which some pathogens inhibit it. As shown, a line ending inan arrow indicates a general tendency to stimulate, while a line endingin a bar indicates a general tendency to inhibit. The diagramillustrates some of the ways by which pathogens can inhibit apoptosis toprevent premature death of the host cells.

FIG. 5 is a simplified diagram depicting the pathway involving heatshock and other stress responses, as well as its interactions with somepathogens. As shown, a line ending in an arrow indicates a generaltendency to stimulate, while a line ending in a bar indicates a generaltendency to inhibit.

FIG. 6 is a diagram representing how parts of the interferon andapoptosis pathways can be combined to create a novel dsRNA-activatedcaspase or related treatments that selectively kill pathogen-infectedcells. A chimeric (pro)caspase protein with a dsRNA-binding domain suchas that from PKR will selectively kill infected cells. Alternatively, asmall-molecule drug that binds both dsRNA (e.g., lividomycin) andcaspases (e.g., by mimicking the caspase-binding region of APAF-1 orFADD) will selectively kill infected cells by crosslinking and therebyactivating endogenous caspases when dsRNA is present.

FIG. 7 is an outline of a polymerase chain reaction (PCR) strategy forthe synthesis of a dsRNA-activated caspase. PCR was used to produce PCRproduct 7. The dsRNA-binding domain from PKR (amino acids 1-174) isfused in frame with a short flexible polypeptide linker (S-G-G-G-S-G(SEQ ID NO: 1)) and full-length caspase-3. A Kozak sequence and stopcodon are included as shown. BamH I and Mlu I restriction sites areincluded at the polynucleotide ends for insertion into an appropriatevector.

FIG. 8 is an outline of a PCR strategy used to produce PCR product 8,another novel dsRNA-activated caspase. The dsRNA-binding domain from PKR(amino acids 1-174) and part of the natural linker region from PKR(amino acids 175-181) are fused in frame with full-length caspase-3. AKozak sequence and stop codon are included as shown. BamH I and Mlu Irestriction sites are included at the polynucleotide ends for insertioninto an appropriate vector.

FIG. 9 is an outline of a PCR strategy used to produce PCR product 9, anovel dsRNA-activated caspase activator. The dsRNA-binding domain fromPKR (amino acids 1-174) and part of the natural linker region from PKR(amino acids 175-181) are fused in frame with amino acids 1-125 of FADD,which includes the death effector domain (DED) that binds toprocaspase-8. A Kozak sequence and stop codon are included as shown.BamH I and Mlu I restriction sites are included at the polynucleotideends for insertion into an appropriate vector.

FIG. 10 is an outline of a PCR strategy used to produce PCR product 10,another novel dsRNA-activated caspase activator. The dsRNA-bindingdomain from PKR (amino acids 1-174) is fused in frame with a shortflexible polypeptide linker (S-G-G-G-S-G (SEQ ID NO: 1)) and amino acids1-125 of FADD, which includes the death effector domain (DED) that bindsto procaspase 8. A Kozak sequence and stop codon are included as shown.BamH I and Mlu I restriction sites are included at the ends for ease ofinsertion into a vector.

FIG. 11, on the left panel, is a schematic diagram of a Clontech vector(pTRE2hyg), into which PCR products 7 through 10, encoding fourdifferent versions of the dsRNA-activated caspase (or caspaseactivator), are inserted by using the BamH I and Mlu I restrictionsites. The vector includes a doxycycline or tetracycline-induciblepromoter for the inserted gene, as well as a hygromycin resistance genefor selection of transfected cells. A Clontech-supplied control vectorhas a luciferase gene inserted after the inducible promoter. All vectorswith inserted genes were linearized by digestion with an Fsp Irestriction enzyme before transfection. Linearized DNA constructscontaining PCR products 7 through 10 and control vector wereelectrophoresed on an agarose gel as shown in the photograph in theright panel. DNA size markers are in the left-most lane.

FIG. 12 is a schematic diagram of the linearized vectors with insertedPCR 7, 8, 9, 10, or luciferase transfected into a Clontech Tet-On™ HeLahuman cell line, which contains the rtTA regulatory protein necessaryfor the proper functioning of the tetracycline or doxycycline-induciblepromoters. The transfected cells are continuously cultured in thepresence of hygromycin to kill any cells without the transfected genes.The resulting cells have the transfected genes stably integrated intotheir genomes and express them in response to doxycycline.

FIG. 13 is a Western blot analysis. Doxycycline induces cellstransfected with PCR-7-containing vectors to express the correspondingdsRNA-activated caspase. Clonal populations of transfected cells wereisolated by limiting dilutions. Cells are cultured with either 10 μg/mldoxycyline or no doxycline for two days, and then Western blots are usedto probe the cell extracts with anti-caspase-3 antibodies. The 32-kDanatural (pro)caspase 3 is visible in all the cells, either with orwithout doxycycline. For each cell clone shown, doxycycline up-regulatesthe expression of the transfected dsRNA-activated caspase, which hasapproximately the predicted size and contains caspase-3 epitopesrecognized by the antibodies.

FIG. 14 are Western blot analyses. Doxycycline induces cells transfectedwith PCR-8-containing vectors to express the correspondingdsRNA-activated caspase. Clonal populations of transfected cells wereisolated by limiting dilutions. The cells were cultured with either 10μg/ml doxycyline or no doxycline for two days, and then Western blotswere used to probe the cell extracts with anti-caspase-3 antibodies. The32-kDa natural (pro)caspase 3 is visible in all the cells, either withor without doxycycline. For cell clones 8-9, 8-13, and 8-17, doxycyclineup-regulates the expression of the transfected dsRNA-activated caspase,which has approximately the predicted size and contains caspase-3epitopes recognized by the antibodies.

FIG. 15 is a Western blot analysis. Doxycycline induces cellstransfected with PCR-9-containing vectors to express the correspondingdsRNA-activated caspase activator. Clonal populations of transfectedcells were isolated by limiting dilutions. The cells were cultured witheither 1 μg/ml doxycyline or no doxycline for two days, and then Westernblots were used to probe the cell extracts with anti-FADD antibodies.The 28-kDa natural FADD is visible in all the cells, either with orwithout doxycycline. For each cell clone shown, doxycycline upregulatesexpression of the dsRNA-activated caspase activator, which hasapproximately the predicted size and contains FADD epitopes recognizedby the antibodies.

FIG. 16 is a Western blot analysis. Doxycycline induces cellstransfected with PCR-10-containing vectors to express the correspondingdsRNA-activated caspase activator. Clonal populations of transfectedcells were isolated by limiting dilutions. Cells were cultured witheither 10 μg/ml doxycyline or no doxycline for two days, and thenWestern blots were used to probe the cell extracts with anti-FADDantibodies. The 28-kDa natural FADD is visible in all the cells, eitherwith or without doxycycline. For each cell clone shown, doxycyclineup-regulates expression of the dsRNA-activated caspase activator, whichhas approximately the predicted size and contains FADD epitopesrecognized by the antibodies.

FIG. 17 are Western blot analyses. The concentration of doxycyclinecontrols the level of dsRNA-activated caspase (or caspase activator)expression in transfected cells. Cell clone 7-6 contains PCR 7, clone8-13 contains PCR 8, clone 10-6 contains PCR 10, and 9A is a pool ofclones that contain PCR 9 but are not separated into individual clonalpopulations by limiting dilution. Untransfected HeLa cells were used asa control. Cells were cultured with 0, 0.01, 0.1, 1, or 10 μg/mldoxycyline for two days, and then Western blots were used to probe thecell extracts with anti-caspase-3 or anti-FADD antibodies. Increasingthe doxycycline concentration generally increases the expression levelof the dsRNA-activated caspase (or caspase activator) relative tonatural caspase 3 or FADD.

FIG. 18 is a graph charting the toxicity of dsRNA-activated caspase (PCR7) levels induced by different concentrations of doxycycline assayed.Cells were added to 96-well plates at an initial density of 5×10⁴cells/ml, and different expression levels of the transfected genes wereinduced by adding 0, 0.01, 0.1, 1, or 10 μg/ml doxycyline. The cellnumbers were estimated after three days using CellTiter 96® (Promega),which is metabolized by live cells. After subtracting the backgroundabsorbance without cells, the absorbance at 492 nm was approximatelylinear with the number of live cells. All assays were performed inquadruplicate to reduce statistical variations. At all doxycyclineconcentrations, the metabolism of cell clones 7-1, 7-4, and 7-6 wasapproximately the same as that of untransfected HeLa cells, indicatinglittle or no toxicity.

FIG. 19 is a graph charting the toxicity of dsRNA-activated caspase (PCR8) levels induced by different concentrations of doxycycline assayed.Cells were added to 96-well plates at an initial density of 5×10⁴cells/ml, and different expression levels of the transfected genes wereinduced by adding 0, 0.01, 0.1, 1, or 10 μg/ml doxycyline. The cellnumbers were estimated after three days using CellTiter 96® (Promega),which is metabolized by live cells. After subtracting the backgroundabsorbance without cells, the absorbance at 492 nm was approximatelylinear with the number of live cells. All assays were performed inquadruplicate to reduce statistical variations. At all doxycyclineconcentrations, the metabolism of cell clones 8-9, 8-13, and 8-17 isapproximately the same as that of untransfected HeLa cells, indicatinglittle or no toxicity.

FIG. 20 is a graph charting the toxicity of dsRNA-activated caspaseactivator (PCR 9) levels induced by different concentrations ofdoxycycline assayed. Cells were added to 96-well plates at an initialdensity of 5×10⁴ cells/ml, and different expression levels of thetransfected genes were induced by adding 0, 0.01, 0.1, 1, or 10 μg/mldoxycyline. The cell numbers were estimated after three days usingCellTiter 96® (Promega), which is metabolized by live cells. Aftersubtracting the background absorbance without cells, the absorbance at492 nm was approximately linear with the number of live cells. Allassays were performed in quadruplicate to reduce statistical variations.

FIG. 21 is a graph charting the toxicity of dsRNA-activated caspaseactivator (PCR 10) levels induced by different concentrations ofdoxycycline assayed. Cells were added to 96-well plates at an initialdensity of 5×10⁴ cells/ml, and different expression levels of thetransfected genes were induced by adding 0, 0.01, 0.1, 1, or 10 μg/mldoxycyline. The cell numbers were estimated after three days usingCellTiter 96® (Promega), which is metabolized by live cells. Aftersubtracting the background absorbance without cells, the absorbance at492 nm was approximately linear with the number of live cells. Allassays were performed in quadruplicate to reduce statistical variations.

FIG. 22 are photographs demonstrating dsRNA-activated caspase activityof cell clone 8-13. Cells were cultured either with or without 10 μg/mldoxycycline for two days, and then treated with the Invitrogentransfection reagents LIPOFECTIN® and PLUS reagent either alone or withpoly(I)•poly(C) synthetic dsRNA approximately 20 hours prior tophotographing. Healthy cells tend to spread out, whereas apoptotic cellsround up and appear to have bright granulated interiors. Cells withoutdsRNA appear healthy, regardless of doxycycline treatment (top left andbottom left photographs). Cells without doxycyline but with dsRNA appeargenerally healthy but include some apoptotic cells (top, rightphotograph), possibly due to the low-level expression of thedsRNA-activated caspase even in the absence of doxycycline. Cells withboth doxycycline and dsRNA exhibit widespread apoptosis as expected(bottom, right photograph).

FIG. 23 are photographs demonstrating dsRNA-activated caspase activityof cell clone 8-9. Cells were cultured either with or without 10 μg/mldoxycycline for two days, and then treated with the Invitrogentransfection reagents LIPOFECTIN® and PLUS reagent either alone or withpoly(I)•poly(C) synthetic dsRNA approximately 20 hours prior tophotographing. Healthy cells tend to spread out, whereas apoptotic cellsround up and appear to have bright granulated interiors. Cells withoutdsRNA appear healthy, regardless of doxycycline treatment (top left andbottom left photographs). Cells without doxycyline but with dsRNA appeargenerally healthy but include some apoptotic cells (top, rightphotograph), possibly due to the low-level expression of thedsRNA-activated caspase even in the absence of doxycycline. Cells withboth doxycycline and dsRNA exhibit widespread apoptosis as expected(bottom, right photograph).

FIG. 24 are photographs demonstrating HeLa cells not transfected with adsRNA-activated caspase construct (control cells). Cells were culturedeither with or without 10 μg/ml doxycycline for two days, and thentreated with the Invitrogen transfection reagents LIPOFECTIN® and PLUSreagent either alone or with poly(I)•poly(C) synthetic dsRNAapproximately 20 hours prior to photographing. Healthy cells tend tospread out, whereas apoptotic cells round up and appear to have brightgranulated interiors. Cells either with or without doxycycline andeither with dsRNA (top right and bottom right photographs) or withoutdsRNA (top left and bottom left photographs) appear generally healthy,with a limited number of round or apoptotic cells visible in each of thefour cases. The widespread apoptosis that was visible in clones 8-9 and8-13 treated with both doxycycline and dsRNA does not occur with theuntransfected HeLa cells.

FIG. 25 is a diagram of an interferon-induced heat shock protein whichselectively protects uninfected cells near infected ones. Aninterferon-induced heat shock protein gene is a new anti-pathogendefense that can be added to cells via gene therapy or other methods toinhibit pathogen replication in cells. Because its effect is localizedin both space and time, only occuring in cells near infected ones,side-effects are minimized.

FIG. 26 is a diagram of an interferon-inducible vector created by addingan interferon-inducible promoter and poly-A sequence to the InvitrogenpCMV/Bsd blasticidin-resistance vector. A multiple cloning sequencebetween the new interferon-inducible promoter and poly-A sequencepermits one to add any gene, such as genes for heat shock proteinsHdj-1, Hsp70, Hsp90, luciferase (as a control), or other genes withanti-pathogen effects.

FIG. 27 is an outline of a PCR strategy used to produce the SV40 poly-Asequence copied from pCMV/Bsd via PCR with the illustrated primers (PCRproduct 11). PCR product 11 is then inserted into pCMV/Bsd as shown tocreate a second poly-A sequence in the vector.

FIG. 28 is an outline of a PCR strategy used to produce PCR product 12.An interferon-inducible promoter containing multipleinterferon-stimulated response elements (ISREs) is cloned from theStratagene vector pISRE-Luc using the PCR primers shown in the figure.PCR product 12 is inserted into the modified pCMV/Bsd containing thesecond poly-A sequence, resulting in a general-purposeinterferon-inducible vector, pCMV/Bsd/ISRE. Any desired gene can beinserted into this new interferon-inducible vector.

FIG. 29 is an outline of a PCR strategy used to produce PCR product 13.The gene for heat shock protein Hdj-1 (NCBI Accession # X62421) iscloned in PCR 13, and the PCR primers are used to add a Kozak sequenceas well as BssH II and Mlu I restriction enzyme sites. PCR product 13containing Hdj-1 is inserted into the vector from FIG. 28, creating aninterferon-inducible Hdj-1 expression vector.

FIG. 30 is an outline of a PCR strategy used to produce PCR product 14.The gene for heat shock protein Hsp70 (NCBI Accession # M11717 M15432)is cloned in PCR 14, and the PCR primers are used to add a Kozaksequence as well as BssH II and Mlu I restriction enzyme sites. PCRproduct 14 containing Hsp70 is inserted into the vector from FIG. 28,creating an interferon-inducible Hsp70 expression vector.

FIG. 31 is an outline of a PCR strategy used to produce PCR product 15.The gene for heat shock Hsp90 (NCBI Accession # M16660) is cloned in PCR15, and the PCR primers are used to add a Kozak sequence as well as BssHII and Mlu I restriction enzyme sites. PCR product 15 containing Hsp90is inserted into the vector from FIG. 28, creating aninterferon-inducible Hsp90 expression vector.

FIG. 32 is an outline of a PCR strategy used to produce PCR product 16.The luciferase gene is cloned from the Stratagene vector pISRE-Luc inPCR 16, and the PCR primers are used to add a Kozak sequence as well asBssH II and Mlu I restriction enzyme sites. PCR product 16 containingthe luciferase gene is inserted into the vector from FIG. 28, creatingan interferon-inducible luciferase expression vector.

FIG. 33 is a diagram of interferon-induced heat shock proteins andphotographs of PCR products 11 through PCR 16 electrophoresed on anagarose gel. PCR 11 is the poly-A sequence, PCR 12 is theISRE-containing interferon-inducible promoter, PCR 13 is Hdj-1, PCR 14is Hsp70, PCR 15 is Hsp90, and PCR16 is luciferase.

FIG. 34 is a photograph of a DNA electrophoresis agarose gel of theinteferon-inducible vectors and genes. Lane 1 is a DNA size marker. Lane2 is the completed interferon-inducible vector pCMV/Bsd/ISRE without aninserted gene. Lane 3 is the same vector with Hsp90 inserted, and Lane 4is the vector with luciferase inserted. The vector in these lanes hasbeen digested with the restriction enzymes Bss HII and Mlu I foranalysis. Lane 5 is a DNA size marker. Lanes 6 and 7 are the Hdj-1 andHsp70 genes inserted into the Invitrogen TOPO vector, respectively,digested with Eco RI for analysis. Using the methods illustrated inFIGS. 29 and 30, the Hdj-1 and Hsp70 genes are inserted intopCMV/Bsd/ISRE.

FIG. 35 is a diagram of an interferon-inducible heat shock protein (HSP)expression vector on the left panel and on the right panel is aphotograph of interferon-inducible HSP expression vectorselectrophoresed on an agarose gel.

FIG. 36 is a diagram of other anti-pathogen effectors that can be addedto cells, and induced by interferon, dsRNA, LPS, apoptosis signals, orother pathogen detection methods, or alternatively, the anti-pathogeneffectors can be constitutively present or active. For example,interferon can induce a gene for bacterial RNase III or one of itseukaryotic homolog dsRNases, which degrade viral dsRNA while leavingcellular RNA relatively intact. Or, one or more endosome inhibitors canbe used to inhibit the uncoating of a virus in the endosome. Examples ofendosome inhibitors include, but are not limited to, vacuolar H⁺-ATPaseinhibitors (such as the human papillomavirus 16 E5 protein, a defectiveATPase subunit, or bafilomycin A1) or vesicular trafficking inhibitors(such as the Salmonella SpiC protein). Alternatively, expression of anuclear localization signal (NLS) inhibitor can be induced by interferonin order to prevent transport of pathogens or pathogen components withNLSs into the nucleus. The NLS inhibitor can be a truncated version ofimportin-alpha that binds to an NLS but is not transported into thenucleus, or it can be any other NLS-binding protein that is nottransported into the nucleus. Proteins with an NLS, or other decoyproteins that bind to importin-alpha, can be overexpressed in thepresence of interferon as another method of inhibiting pathogen NLSs.

FIG. 37 is a Western blot analysis. Doxycycline induces 8S cells toexpress the dsRNA-activated caspase. Untransfected H1-HeLa cells werecultured without doxycycline for two days, and 8S cells were culturedwith 0, 1, or 10 μg/ml doxycycline for two days. Western blots were thenused to probe the cell extracts with anti-caspase-3 antibodies. The32-kDa natural (pro)caspase 3 was visible in all the cells, regardlessof transfection or doxycycline. For 8S cells, 1 or 10 μg/ml doxycyclineupregulated expression of the dsRNA-activated caspase, which hasapproximately the predicted size (FIG. 37, labeled 53 kDa new protein)and contains caspase-3 epitopes recognized by the antibodies.

FIG. 38 are photographs demonstrating the effectiveness ofdsRNA-activated caspase against virus. Control untransfected H1-HeLacells without doxycycline and 8S H1-HeLa cells induced with 10 μg/mldoxycycline were grown in 25-cm² tissue culture flasks. Cells wereinfected with human rhinovirus 14 (American Type Culture Collection(ATCC) number VR-284) (FIG. 38, lower left and right panels). After 7days of incubation at 33° C., all untransfected cell populations exposedto rhinovirus were dead and detached from their flasks' surfaces (FIG.38, lower left panel). In contrast, transfected 8S H1-HeLa cells thathave been exposed to rhinovirus were alive, attached, and confluent, andthey show no signs of infection (FIG. 38, lower right panel). Bothuntransfected and transfected cells not exposed to rhinovirus were alsoconfluent and healthy (FIG. 38, upper left and right panels,respectively).

FIG. 39 is a Western blot analysis. Doxycycline induces 293 cellstransfected with the PCR-7- or PCR-8-containing vectors to express thecorresponding dsRNA-activated caspase. Cells were cultured with either10 μg/ml doxycycline or no doxycycline for two days, and then Westernblots were used to probe the cell extracts with anti-caspase-3antibodies. The 32-kDa natural (pro)caspase 3 was visible in all thecells, either with or without doxycycline. For each cell clone shown,doxycycline upregulated expression of the dsRNA-activated caspase, whichhas approximately the predicted size (FIG. 39, labeled as 53 kDa newprotein) and contains caspase-3 epitopes recognized by the antibodies.

FIG. 40 is a Western blot analysis. Doxycycline induces 293 cellstransfected with the PCR-9-containing vector to express thecorresponding dsRNA-activated caspase activator. Cells were culturedwith either 10 μg/ml doxycycline or no doxycycline for two days, andthen Western blots were used to probe the cell extracts with anti-FADDantibodies. The 28-kDa natural FADD was visible in all the cells, eitherwith or without doxycycline. For each cell clone shown, doxycyclineupregulated expression of the dsRNA-activated caspase activator, whichhas approximately the predicted size (FIG. 40, labeled as 41 kDa newprotein) and contains FADD epitopes recognized by the antibodies.

FIG. 41 is a Western blot analysis. Doxycycline induces 293 cellstransfected with the PCR-10-containing vector to express thecorresponding dsRNA-activated caspase activator. Cells were culturedwith either 10 μg/ml doxycycline or no doxycycline for two days, andthen Western blots were used to probe the cell extracts with anti-FADDantibodies. The 28-kDa natural FADD was visible in all the cells, eitherwith or without doxycycline. For each cell clone shown, doxycyclineupregulated expression of the dsRNA-activated caspase activator, whichhas approximately the predicted size (FIG. 41, labeled as 41 kDa newprotein) and contains FADD epitopes recognized by the antibodies.

FIG. 42 is a diagram of the synthesis strategy for PCR product 25, whichencodes a novel pathogen-activated caspase activator.2′,5′-oligoadenylate is produced within cells in response to pathogencomponents such as dsRNA. The 2′,5′-oligoadenylate-binding domain fromRNase L (amino acids 1-335) was fused in frame with a short flexiblepolypeptide linker (amino acid sequence S-G-G-G-S-G (SEQ ID NO: 1)) andamino acids 1-97 of Apaf-1, which included the caspase recruitmentdomain (CARD) that binds to procaspase 9. A Kozak sequence and stopcodon were included, as shown. BamH I and Mlu I restriction sites wereincluded at the ends for ease of insertion into the pTRE2hyg vector. PCR21 used the indicated 5′ and 3′ PCR primers to copy the region encodingamino acids 1-335 of RNase L from the provided plasmid. PCR 22 used theindicated 5′ and 3′ PCR primers to copy the region encoding amino acids1-97 of Apaf-1 from the provided plasmid. PCR 25 used the gel-purifiedproducts of PCR 21 and 22, 5′ primer from PCR 21, and 3′ primer from PCR22 to create the desired product via splicing by overlap extension (C.W. Dieffenbach and G. S. Dveksler (eds.), PCR Primer: A LaboratoryManual, 1995, Cold Spring Harbor Laboratory Press, Plainview, N.Y.).

FIG. 43 is a diagram of the synthesis strategy for PCR product 26, whichencodes a novel pathogen-activated caspase activator. Lipopolysaccharide(LPS) is a component of pathogens such as bacteria. The LPS-bindingdomain from BPI (amino acids 1-199) was fused in frame with a shortflexible polypeptide linker (amino acid sequence S-G-G-G-S-G (SEQ ID NO:1)) and amino acids 1-97 of Apaf-1, which included the caspaserecruitment domain (CARD) that binds to procaspase 9. A Kozak sequenceand stop codon were included, as shown. BamH I and Mlu I restrictionsites were included at the ends for ease of insertion into the pTRE2hygvector. PCR 23 used the indicated 5′ and 3′ PCR primers to copy theregion encoding amino acids 1-199 of BPI from the provided plasmid. PCR22 used the indicated 5′ and 3′ PCR primers to copy the region encodingamino acids 1-97 of Apaf-1 from the provided plasmid. PCR 26 used thegel-purified products of PCR 22 and 23, 5′ primer from PCR 23, and 3′primer from PCR 22 to create the desired product via splicing by overlapextension.

FIG. 44 is a diagram of the synthesis strategy for PCR product 27, whichencodes a novel dsRNA-activated caspase activator. The dsRNA-bindingdomain from PKR (amino acids 1-174) and part of the natural linkerregion from PKR (amino acids 175-181) were fused in frame with aminoacids 1-97 of Apaf-1, which included the caspase recruitment domain(CARD) that binds to procaspase 9. When two or more copies of theprotein encoded by PCR 27 are crosslinked by dsRNA, they will crosslinkand activate endogenous (pro)caspase 9. A Kozak sequence and stop codonwere included, as shown. BamH I and Mlu I restriction sites wereincluded at the ends for ease of insertion into the pTRE2hyg vector. PCR3 used the indicated 5′ and 3′ PCR primers to copy the region encodingamino acids 1-181 of PKR from the provided plasmid. PCR 24 used theindicated 5′ and 3′ PCR primers to copy the region encoding amino acids1-97 of Apaf-1 from the provided plasmid. PCR 27 used the gel-purifiedproducts of PCR 3 and 24, 5′ primer from PCR 3, and 3′ primer from PCR24 to create the desired product via splicing by overlap extension.

FIG. 45 is a diagram of the synthesis strategy for PCR product 28, whichencodes a novel pathogen-activated caspase. 2′,5′-oligoadenylate isproduced within cells in response to pathogen components such as dsRNA.The 2′,5′-oligoadenylate-binding domain from RNase L (amino acids 1-335)was fused in frame with a short flexible polypeptide linker (amino acidsequence S-G-G-G-S-G (SEQ ID NO: 1)) and full-length caspase 3. A Kozaksequence and stop codon were included, as shown. BamH I and Mlu Irestriction sites were included at the ends for ease of insertion intothe pTRE2hyg vector. PCR 21 used the indicated 5′ and 3′ PCR primers tocopy the region encoding amino acids 1-335 of RNase L from the providedplasmid. PCR 2 used the indicated 5′ and 3′ PCR primers to copy thecoding sequence of caspase 3 from the provided plasmid. PCR 28 used thegel-purified products of PCR 21 and 2, 5′ primer from PCR 21, and 3′primer from PCR 2 to create the desired product via splicing by overlapextension.

FIG. 46 is a diagram of the synthesis strategy for PCR product 29, whichencodes a novel pathogen-activated caspase. Lipopolysaccharide (LPS) isa component of pathogens such as bacteria. The LPS-binding domain fromBPI (amino acids 1-199) was fused in frame with a short flexiblepolypeptide linker (amino acid sequence S-G-G-G-S-G (SEQ ID NO: 1)) andfull-length caspase 3. A Kozak sequence and stop codon were included, asshown. BamH I and Mlu I restriction sites were included at the ends forease of insertion into the pTRE2hyg vector. PCR 23 used the indicated 5′and 3′ PCR primers to copy the region encoding amino acids 1-199 of BPIfrom the provided plasmid. PCR 2 used the indicated 5′ and 3′ PCRprimers to copy the coding sequence of caspase 3 from the providedplasmid. PCR 29 used the gel-purified products of PCR 23 and 2, 5′primer from PCR 23, and 3′ primer from PCR 2 to create the desiredproduct via splicing by overlap extension.

FIG. 47, left panel, is a schematic diagram of a Clontech vector(pTRE2hyg), into which Bam HI and Mlu I restriction enzyme digested PCRproducts 25, 26, 27, 28, and 29 were ligated into the vector to createexpression vectors for PCR 25, 26, 27, 28, and 29. The vectors include adoxycycline or tetracycline-inducible promoter for the inserted gene, aswell as a hygromycin resistance gene for selection of transfected cells.All of the vectors with the inserted genes were linearized fortransfection using the Fsp I restriction enzyme as shown in the DNA gelelectrophoresis photograph in the right panel. DNA size markers are inthe left-most lane.

FIG. 48 is a schematic of further chimeric caspases.

FIG. 49 is an illustration of examples of chimeric proteins.

FIGS. 50 (a)-(f) are illustrations of examples of chimeric transcriptionfactors.

FIG. 51 is a schematic of using IFN-induced defenses. Illustrated is avector with an ISRE-containing promoter regulating the expression of atleast one defense gene.

FIG. 52 demonstrates the synthesis strategy for a truncated importin α1gene and its insertion into the pCMV/Bsd/ISRE vector to produce the newvector pCMV/Bsd/ISRE/α1. It encodes a truncated version of importin α1that lacks the importin-β-binding domain.

FIG. 53 is a schematic for the production of PCR product 30. It encodesa truncated form of importin α1 that lacks the importin-β-binding domainbut includes an HA epitope.

FIG. 54 illustrates the synthesis strategy for a truncated importin α4gene and its insertion into the pCMV/Bsd/ISRE vector to produce the newvector pCMV/Bsd/ISRE/α4. It encodes a truncated version of importin α4that lacks the importin-β-binding domain.

FIG. 55 is a schematic for the production of PCR product 31. It encodesa truncated form of importin α4 that lacks the importin-β-binding domainbut includes an HA epitope.

FIG. 56 illustrates the synthesis strategy for a truncated importin α6gene and its insertion into the pCMV/Bsd/ISRE vector to produce the newvector pCMV/Bsd/ISRE/α6. It encodes a truncated version of importin α6that lacks the importin-α-binding domain.

FIG. 57 is a schematic for the production of PCR product 32. PCR wascarried out using the illustrated PCR primers and the vectorpCMV/Bsd/ISRE/α6. It encodes a truncated form of importin α6 that lacksthe importin-β-binding domain but includes an HA epitope.

FIG. 58 illustrates the creation of a gene encoding E. coli RNase IIIwith an HA epitope, and its subsequent insertion into the pCMV/Bsd/ISREvector to produce the new vector pCMV/Bsd/ISRE/RNase III.

FIG. 59 is a schematic for the production of PCR product 33. PCR wascarried out using the illustrated PCR primers and the vectorpCMV/Bsd/ISRE/RNase III. It encodes E. coli RNase I with an HA epitope.

FIG. 60 is a schematic for the insertion of a gene encoding the HPV-16E5 protein into the pCMV/Bsd/ISRE vector to produce the new vectorpCMV/Bsd/ISRE/E5.

FIG. 61 is a schematic for the production of PCR product 34. PCR wascarried out using the illustrated PCR primers and the vectorpCMV/Bsd/ISRE/E5. It encodes the HPV-16 E5 protein.

FIG. 62 illustrates the synthesis strategy for a gene encoding theSalmonella SpiC protein with an HA epitope, and its subsequent insertioninto the pCMV/Bsd/ISRE vector to produce the new vectorpCMV/Bsd/ISRE/SpiC.

FIG. 63 is a schematic for the production of PCR product 35. It encodesthe Salmonella SpiC protein with an HA epitope.

FIG. 64 is a schematic for the production of PCR product 36. PCR wascarried out using the illustrated PCR primers and the vectorpCMV/Bsd/ISRE/Hdj1. The resulting PCR product 36 has Bam HI and Mlu Irestriction sites for ease of insertion into the pTRE2hyg vector. Itencodes human Hdj-1, also known as Hsp40.

FIG. 65 is a schematic for the production of PCR product 37. Theresulting PCR product 37 has Bam HI and Mlu I restriction sites for easeof insertion into the pTRE2hyg vector. It encodes human Hsp70.

FIG. 66 is a schematic for the production of PCR product 38. It encodeshuman Hsp90.

FIG. 67 is a photograph of the linearized vectors with the insertedproducts PCR 30-38 for transfection after electrophoresis in an agarosegel. The far left lane contains a DNA size marker.

FIG. 68 illustrates schematically how to produce test proteins thatcontain protein transduction domains or tags.

FIG. 69 illustrates PCR primers for producing a DNA sequence encodingaequorin fused to one of the following protein transduction tags: TAT,PTD-4, an arginine-rich sequence Arg, or no protein transduction tag.

FIG. 70 illustrates PCR primers for producing a DNA sequence encodingenhanced green fluorescent protein (EGFP) fused to one of the followingprotein transduction tags: TAT, PTD-4, an arginine-rich sequence Arg, orno protein transduction tag.

FIG. 71 illustrates PCR primers for producing a DNA sequence thatincludes the coding sequence from PCR product 7 or 8 fused to one of thefollowing protein transduction tags: TAT, PTD-4, an arginine-richsequence Arg, or no protein transduction tag.

FIG. 72 illustrates PCR primers for producing a DNA sequence thatincludes the coding sequence from PCR product 9 or 10 fused to one ofthe following protein transduction tags: TAT, PTD-4, an arginine-richsequence Arg, or no protein transduction tag.

FIG. 73 illustrates PCR primers for producing a DNA sequence thatincludes the coding sequence from PCR product 25 fused to one of thefollowing protein transduction tags: TAT, PTD-4, an arginine-richsequence Arg, or no protein transduction tag.

FIG. 74 illustrates PCR primers for producing a DNA sequence thatincludes the coding sequence from PCR product 26 fused to one of thefollowing protein transduction tags: TAT, PTD-4, an arginine-richsequence Arg, or no protein transduction tag.

FIG. 75 illustrates PCR primers for producing a DNA sequence thatincludes the coding sequence from PCR product 27 fused to one of thefollowing protein transduction tags: TAT, PTD-4, an arginine-richsequence Arg, or no protein transduction tag.

FIG. 76 illustrates PCR primers for producing a DNA sequence thatincludes the coding sequence from PCR product 28 fused to one of thefollowing protein transduction tags: TAT, PTD-4, an arginine-richsequence Arg, or no protein transduction tag.

FIG. 77 illustrates PCR primers for producing a DNA sequence thatincludes the coding sequence from PCR product 29 fused to one of thefollowing protein transduction tags: TAT, PTD-4, an arginine-richsequence Arg, or no protein transduction tag.

FIG. 78 illustrates PCR primers for producing a DNA sequence thatincludes the coding sequence from PCR product 30 fused to one of thefollowing protein transduction tags: TAT, PTD-4, an arginine-richsequence Arg, or no protein transduction tag.

FIG. 79 illustrates PCR primers for producing a DNA sequence thatincludes the coding sequence from PCR product 31 fused to one of thefollowing protein transduction tags: TAT, PTD-4, an arginine-richsequence Arg, or no protein transduction tag.

FIG. 80 illustrates PCR primers for producing a DNA sequence thatincludes the coding sequence from PCR product 32 fused to one of thefollowing protein transduction tags: TAT, PTD-4, an arginine-richsequence Arg, or no protein transduction tag.

FIG. 81 illustrates PCR primers for producing a DNA sequence thatincludes the coding sequence from PCR product 33 fused to one of thefollowing protein transduction tags: TAT, PTD-4, an arginine-richsequence Arg, or no protein transduction tag.

FIG. 82 illustrates PCR primers for producing a DNA sequence thatincludes the coding sequence from PCR product 34 fused to one of thefollowing protein transduction tags: TAT, PTD-4, an arginine-richsequence Arg, or no protein transduction tag.

FIG. 83 illustrates PCR primers for producing a DNA sequence thatincludes the coding sequence from PCR product 35 fused to one of thefollowing protein transduction tags: TAT, PTD-4, an arginine-richsequence Arg, or no protein transduction tag.

FIG. 84 illustrates PCR primers for producing a DNA sequence thatincludes the coding sequence from PCR product 36 fused to one of thefollowing protein transduction tags: TAT, PTD-4, an arginine-richsequence Arg, or no protein transduction tag.

FIG. 85 illustrates PCR primers for producing a DNA sequence thatincludes the coding sequence from PCR product 37 fused to one of thefollowing protein transduction tags: TAT, PTD-4, an arginine-richsequence Arg, or no protein transduction tag.

FIG. 86 illustrates PCR primers for producing a DNA sequence thatincludes the coding sequence from PCR product 38 fused to one of thefollowing protein transduction tags: TAT, PTD-4, an arginine-richsequence Arg, or no protein transduction tag.

DETAILED DESCRIPTION OF THE INVENTION

Organisms, such as humans, other animals, and plants, and their cellshave natural defenses against pathogens, such as viruses, viroids,bacteria, rickettsia, chlamydia, mycoplasma, fungi, protozoa, helminths,and prions. These natural defenses include, for example and withoutlimitation: (1) the interferon pathway, by which an infected cell canwarn or prime nearby uninfected cells to increase their resistance toinfection; (2) apoptosis, in which an infected cell can commit cellsuicide to prevent further spread of the infection; (3) heat shock andother stress responses, which help cells survive under stressconditions, such as infection; (4) inflammatory responses, which cancombat infections; (5) unfolded-protein responses or endoplasmicreticulum-associated protein degradation responses, which help cellsrespond to endoplasmic reticulum stress or protein accumulation, such ascan be caused by a pathogen; (6) innate immune responses, which inhibita broad spectrum of pathogens; and (7) adaptive immune responses, whichidentify and respond to specific pathogens.

However, many pathogens, for example: viruses such as variola major(smallpox), Ebola, HIV, hepatitis viruses, influenza viruses,papillomaviruses, herpesviruses, and adenoviruses; bacteria such asMycobacterium species, Salmonella species, Yersinia species, Chlamydiaspecies, Coxiella burnetti, Francisella tularensis, Brucella species,Bordetella species, Listeria monocytogenes, and Legionella pneumophila;fungi such as Histoplasma capsulatum; and protozoa such as Plasmodiumspecies, Trypanosoma species, Leishmania species, and Toxoplasma gondii,have developed methods to evade some or all of these natural defenses.

This invention provides chimeric molecules, agents, and methods of usethereof, which manipulate or modify the natural defenses to be moreeffective against pathogen infections. This invention is also known as“Pharmacological Augmentation of Nonspecific Anti-pathogen CellularEnzymes and Activities (PANACEA).”

A chimeric molecule of the invention, as described herein, is composedof at least two domains, said domains being not normally found inassociation together, or bound to one another, in a cell.

An agent of the invention, as described herein, is one that isnon-naturally-occurring in a cell.

A broad spectrum of pathogens will be susceptible to treatment with theagents and chimeric molecules described herein, and include, for exampleand without limitation: viruses, including those belonging to thefamilies of poxvirus (such as variola major), herpesvirus (such asherpes simplex virus types 1 and 2, varicella-zoster virus,cytomegaloviruses, and Epstein-Barr virus), adenovirus (such as varioushuman adenovirus serotypes), papovavirus (such as humanpapillomaviruses), hepadnavirus (such as hepatitis B virus), parvovirus(such as parvovirus-like agent), picornavirus (such as poliovirus,Coxsachie viruses A and B, rhinoviruses, and foot-and-mouth diseasevirus), calicivirus (such as Norwalk agent and hepatitis E virus),togavirus (such as equine encephalitis viruses and rubella virus),flavivirus (such as West Nile virus, yellow fever virus, and Powassan),coronavirus (such as human coronaviruses), reovirus (such as Coloradotick fever virus), rhabdovirus (such as rabies virus), filovirus (suchas Ebola and Marburg viruses), paramyxovirus (such as parainfluenzaviruses, measles, distemper, rinderpest, and respiratory syncytialvirus), orthomyxovirus (such as influenza viruses), bunyavirus (such asRift Valley fever virus and Hantaan virus), arenavirus (such as Lassavirus), retrovirus (such as human immunodeficiency virus and human Tcell leukemia virus), plant viruses, for example: dsDNA plant viruses(such as cauliflower mosaic virus and badnaviruses); ssDNA plant viruses(such as geminiviruses); dsRNA plant viruses (such as plant reovirusesand cryptoviruses); negative-sense or ambisense RNA plant viruses (suchas rhabdoviruses, tomato spotted wilt virus, and tenuiviruses);positive-sense ssRNA plant viruses (such as tobacco mosaic virus,tobacco rattle virus, and alfalfa mosaic virus); and viroids (such aspotato spindle tuber viroid); and other hepatitis viruses or otherviruses; bacteria, such as Treponema pallidum, Borrelia bergdorferi,Helicobacter pylori, Pseudomonas aeruginosa, Legionella pneumophila,Neisseria meningitidis, Neisseria gonorrhoeae, Brucella species,Bordetella pertussis, Francisella tularensis, Escherichia coli, Shigelladysenteriae, Salmonella species, Klebsiella pneumoniae, Proteus species,Yersinia species, Vibrio cholerae, Haemophilus influenzae, Rickettsiaspecies, Coxiella burnetii, Chlamydia species, Mycoplasma species,Staphylococcus species, Streptococcus species, Bacillus anthracis,Clostridium species, Listeria monocytogenes, Corynebacteriumdiphtheriae, Mycobacterium tuberculosis, Mycobacterium leprae, and otherMycobacterium species, and Nocardia asteroides; prions, such as thecausitive agents of kuru, Creutzfeldt-Jakob disease,Gerstmann-Straussler syndrome, scrapie, bovine spongiformencephalopathy, and transmissible mink encephalopathy; protozoa, such asPlasmodium vivax, Plasmodium ovale, Plasmodium malariae, Plasmodiumfalciparum, Toxoplasma gondii, Pneumocystis carinii, Trypanosoma cruzi,Trypanasoma brucei gambiense, Trypanasoma brucei rhodesiense, Leishmaniaspecies, Naegleria, Acanthamoeba, Trichomonas vaginalis, Cryptosporidiumspecies, Isospora species, Balantidium coli, Giardia lamblia, Entamoebahistolytica, and Dientamoeba fragilis; fungi, such as Candida albicans,Candida parasilosis, Cryptococcus neoformans, Apergillus fumigatusconidia and Aspergillus fumigatus hyphae; or multicellular parasitesincluding Trichinella spiralis, nematode larvae, Schistosome larvae,Ascaris, Tricuris, filarila worms and the like.

As used herein, a pathogen, which can be detected by a chimeric moleculeor agent of the invention, include those parts of the pathogen that aresufficient for their detection by the chimeric molecule or agent. Forexample, a pathogen component, a pathogen product or an epitope that ispathogen-specific are all encompassed by the term pathogen as usedherein.

A pathogen-detection domain, as used herein, is generally directed to adomain that is capable of recognizing or binding a pathogen, pathogencomponent or product of the pathogen. As used herein, the termpathogen-detection domain is a region of the molecule that includes atleast the minimal region necessary to perform the pathogen recognition(also referred to herein as pathogen detection) function of the domain.The pathogen-detection domain can also be encompassed within a largerregion or structure, or smaller region or structure, but it stillretains the pathogen recognition function of the domain.

More particularly, a detector domain, as used herein, is a molecule thatbinds to, is stimulated by, or is inhibited by one or more of thefollowing: a pathogen (such as, for example, an extracellular domain ofa toll-like receptor that binds to bacteria or other pathogens); apathogen component (such as, for example, the domain from approximatelyamino acids 1-199 of human bactericidal/permeability-increasing protein(BPI) that binds to bacterial lipopolysaccharide (LPS)); apathogen-produced product (such as, for example, the domain fromapproximately amino acids 1-174 of human PKR that binds to dsRNAproduced in virus-infected cells); a pathogen-induced product (such as,for example, the domain from approximately amino acids 1-335 of humanRNase L that binds to 2′,5′-oligoadenylate produced in virus-infectedcells); or a pathogen-induced signaling molecule (such as, for example,the domain from approximately amino acids 98-1194 that binds tocytochrome c during pathogen-induced apoptotic pathway signaling). Amolecule or structure that is detected can belong to multiple categoriesdescribed supra. For example, dsRNA can be considered a pathogencomponent, a pathogen-produced product, or a pathogen-induced product.

Pathogen-detection domains can be isolated from naturally-occurringmolecules that normally recognize a pathogen, pathogen component orproduct of said pathogen, such as a cellular protein. Suitablepathogen-detection domains can be isolated from a wide range of knowncellular proteins from a number of different organisms, including forexample, humans, non-human primates, rodents, plants, Drosophila, yeast,bacteria and the like, as will be appreciated by one of skill in theart. Alternatively, the pathogen-detection domain can besynthetically-derived, such as by chemically modifying anaturally-occurring molecule, or otherwise manipulating anaturally-occurring molecule to enhance, optimize, or modify thepathogen-detection domain, using standard techniques known to those ofskill in the art. Additionally, the pathogen-detection domain can be asynthetic product such as a small molecule or a peptidomimetic.Furthermore, a pathogen-detection domain can be an antibody (including,for example, antibody fragments, such as Fab, Fab′, F(ab′)₂, andfragments including either a V_(L) or V_(H) domain, single chainantibodies, bi-specific, chimeric or humanized antibodies), thatrecognizes a specific pathogen epitope, an epitope of a pathogencomponent or an epitope of a product of the pathogen.

In one embodiment, a pathogen, pathogen component or product of thepathogen, to which a pathogen-detection domain of the chimeric moleculeof the invention can bind is double-stranded RNA (dsRNA), which isproduced by said pathogen. In a preferred embodiment, the dsRNA isproduced by a virus or a virus-infected cell.

Suitable dsRNA binding domains can be isolated from a wide range ofknown dsRNA-binding proteins from a number of different organisms,including for example, humans, non-human primates, rodents, plants,Drosophila, yeast, bacteria and the like, as will be appreciated by oneof skill in the art. Examples of dsRNA-binding proteins include proteinkinase R, 2′,5′-oligoadenylate synthases, RNA-specific adenosinedeaminase 1 (ADAR1), vaccinia E3L, RNase III, Rnt1p, and Pac1. Theidentification and isolation of suitable domains from proteins or othermolecules of interest can be readily achieved using standard techniques,as will be appreciated by one of skill in the art.

Examples of some dsRNA binding domain-containing proteins and theapproximate amino acid position of the dsRNA binding domains areprovided in Table 1. The protein, the approximate amino acid location ofthe dsRNA binding domain region within the protein, and the NationalCenter for Biotechnology Information (NCBI) database accession numberare provided in Table 1. TABLE 1 NCBI Accession Protein, organism Domaintype: sequence location (amino acids) number Protein kinase R, Homosapiens dsRNA binding domain: 1-174 AAC50768 Protein kinase R, Musmusculus dsRNA binding domain: 1-160 Q03963 E3L protein, Vaccinia virusdsRNA binding domain: 114-185 B35928 RNase III, E. coli dsRNA bindingdomain: 153-226 NP_417062 RNT1p, Saccharomyces dsRNA binding domain:330-471 S56053 cerevisiae 2′,5′-oligoadenylate synthetase, dsRNA-bindingdomain: 104-158 P00973 41- and 46-kDa forms, Homo sapiens2′,5′-oligoadenylate dsRNA-binding domains: 102-149 P29728 synthetase,69- and 71-kDa and 438-493 forms, Homo sapiens 2′,5′-oligoadenylatedsRNA-binding domains: 103-155, AAD28543 synthetase, 100-kDa form,502-554, and 845-898 Homo sapiens 2′,5′-oligoadenylate synthetasedsRNA-binding domain: 105-159 P11928 1A, Mus musculus ADAR1-a(RNA-specific dsRNA-binding domains: 553-569, U18121 adenosinedeaminase), Homo 664-680, and 776-792 sapiens ADAR1 (RNA-specificdsRNA-binding domains: 457-506, NP_062629 adenosine deaminase), Mus568-617, and 676-741 musculus

dsRNA binding proteins that contain one or more dsRNA binding domainssuitable for use in this invention include, for example and withoutlimitation: 2′,5′-oligoadenylate synthetase 100 kDa form, Homo sapiens(NCBI Accession #AAD28543); 2′,5′-oligoadenylate synthetase 69 and 71kDa forms, Homo sapiens(NCBI Accession #P29728); 2′,5′-oligoadenylatesynthetase 41 and 46 kDa forms, Homo sapiens (NCBI Accession #P00973);2′,5′-oligoadenylate synthetase 1A, Mus musculus (NCBI Accession#P11928); 2′,5′-oligoadenylate synthetase 1B, Mus musculus (NCBIAccession #P29080); 2′,5′-oligoadenylate synthetase 2, Mus musculus(NCBI Accession #SYMS02); 2′,5′-oligoadenylate synthetase 3, Musmusculus (NCBI Accession #SYMS03); RNase III, Homo sapiens (NCBIAccession #AAF80558); RNase III, Escherichia coli (NCBI Accession#NP_(—)417062); Rnt1, Saccharomyces cerevisiae (NCBI Accession #S56053);and Pac1, Schizosaccharomyces pombe (NCBI Accession #S12605).Identification and isolation of a dsRNA binding domain from these or anyother proteins will be readily appreciated by one of skill in the artusing standard techniques.

Other pathogen-detection domains can be isolated from otherdsRNA-binding compounds, including for example, antibiotics such aslividomycin or tobramycin.

A pathogen detection domain can also be a molecule that binds tolipopolysaccharide (LPS), such as the domain of approximately aminoacids 1-197 of LPS-binding protein (LBP) (S. L. Abrahamson et al. (1997)Journal of Biological Chemistry 272, 2149-2155; L. J. Beamer et al.(1998) Protein Science 7, 906-914), the domain of approximately aminoacids 1-193 of bactericidal/permeability-increasing protein (BPI) (S. L.Abrahamson et al. (1997) Journal of Biological Chemistry 272, 2149-2155;L. J. Beamer et al. (1998) Protein Science 7, 906-914), or asingle-chain antibody that binds to LPS.

A pathogen-detection domain can also be a domain that recognizes anepitope which is present in multiple copies or is reiterated on thepathogen, pathogen component or pathogen product.

A pathogen-induced product-detection domain is generally directed to anisolated domain that is capable of recognizing or binding apathogen-induced product. As used herein, the term pathogen-inducedproduct-detection domain is a region of the molecule that includes atleast the minimal region necessary to perform the function of thedomain. The pathogen-induced product-detection domain can also beencompassed within a larger or smaller region or structure, but it stillretains the pathogen-induced product-detection function of the domain.

Pathogen-induced product-detection domains can be isolated fromnaturally-occurring molecules that normally recognize a pathogen-inducedproduct, such as a cellular protein that is induced to be expressed by acell in response to a pathogen or pathogen stimulus. Suitablepathogen-induced product-detection domains can be isolated from a widerange of known cellular proteins from a number of different organisms,including for example, humans, non-human primates, rodents, plants,Drosophila, yeast, bacteria and the like, as will be appreciated by oneof skill in the art. The pathogen-induced product-detection domain canalso be synthetically-derived, such as by chemically modifying anaturally-occurring molecule, or otherwise manipulating anaturally-occurring molecule to enhance, optimize, or modify thepathogen-induced product-detection domain, using standard techniquesknown to those of skill in the art, or alternatively, they can be asynthetic product such as a small molecule or a peptidomimetic.Furthermore, a pathogen-induced product-detection domain can be anantibody (including, for example, antibody fragments, such as Fab, Fab′,F(ab′)₂, and fragments including either a V_(L) or V_(H) domain, singlechain antibodies, bi-specific, chimeric or humanized antibodies), thatrecognizes a specific pathogen-induced product.

A pathogen-induced product which can be recognized by a pathogen-inducedproduct-detection domain includes, for example and without limitation,cytokines such as an interferon or interleukin, 2′,5′-oligoadenylate,unfolded-protein response or endoplasmic reticulum-associated proteindegradation response signaling molecules, stress response orinflammatory response signaling molecules, and apoptosis signalingmolecules.

Cytokines such as interferon alpha, interferon beta, or interferon omegaare produced by cells in response to a pathogen infection and many genesare responsive to stimulation by such cytokines through suitableinducible promoters, for example and without limitation, promoters thatcontain one or more interferon-stimulated response elements (ISREs).Examples of suitable promoters are well known to those of skill in theart and include the promoters of the following genes: protein kinase R(K. L. Kuhen and C. E. Samuel (1999) Virology 254, 182-195; H. Tanakaand C. E. Samuel (2000) Gene 246, 373-382); 2′,5′-oligoadenylatesynthetases (F. Yu, Q. Wang, and G. Floyd-Smith (1999) Gene 237,177-184; G. Floyd-Smith, Q. Wang, and G. C. Sen (1999) Exp. Cell Res.246, 138-147; Q. Wang and G. Floyd-Smith (1998) Gene 222, 83-90); Mxgenes (T. Ronni et al. (1998) J. Interferon Cytokine Res. 18, 773-781);ADAR1 (C. X. George and C. E. Samuel (1999) Gene 229, 203-213). TheISRE-containing promoter of the Stratagene PathDetect® ISRE vector(Stratagene #219092) is another example of a promoter that can beinduced by cytokines such as interferon alpha, interferon beta, orinterferon omega. A pathogen-induced product-detection domain can be anISRE-containing or other suitable promoter as defined supra that isoperatively linked to a polynucleotide sequence encoding an effectordomain as described herein, the effector domain being one not typicallyor normally associated with the promoter.

Cytokines such as interferon gamma, interleukin 1, interleukin 2,interleukin 3, interleukin 4, interleukin 5, interleukin 6, interleukin7, interleukin 9, interleukin 12, or interleukin 15 are produced bycells in response to a pathogen infection, and many genes are responsiveto stimulation by such cytokines through suitable inducible promoters,for example, and without limitation, promoters that contain one or moregamma-activated sequences (GASs), GAS-related sequences, orSTAT-protein-binding sequences. Examples of suitable promoters are wellknown to those of skill in the art (T. Kisseleva et al. (2002) Gene 285,1-24). The GAS-containing promoter of the Stratagene PathDetect® GASvector (Stratagene #219093) is an example of a promoter that can beinduced by cytokines such as interferon gamma. A pathogen-inducedproduct-detection domain can be an GAS-containing promoter, GAS-relatedsequence containing promoter, STAT protein binding sequence-containingpromoter, or other suitable promoter as defined supra that isoperatively linked to a polynucleotide sequence encoding an effectordomain as described herein, the effector domain being one not typicallyor normally associated with the promoter.

In another preferred embodiment, the pathogen-induced product-detectiondomain is a dsRNA-inducible promoter that is responsive todsRNA-stimulated cellular signaling. In one embodiment, the promoter isoperatively linked to a polynucleotide sequence encoding an effectordomain as described herein, said effector domain being one not typicallyor normally associated with said promoter. Examples of suitablepromoters will be appreciated by one of skill in the art and include thepromoters of the following genes: interferon-beta (R. Lin et al. (2000)Molecular and Cellular Biology 20, 6342-6353); RANTES (R. Lin et al.(2000) Molecular and Cellular Biology 20, 6342-6353); and otherinterferon genes (R. M. Roberts et al. (1998) J. Interferon CytokineRes. 18, 805-816).

Optionally, a promoter that is a pathogen-induced product-detectiondomain can be conditionally-regulated. For example, the promoter caninclude a control region that is responsive to drug stimulation, such asan antibiotic. Examples of drug-inducible promoters include atetracycline-inducible or doxycycline-inducible promoter (for example,Clontech pTRE2hyg vector), which is stimulated with the appropriatetranscription factor (for example, Clontech TetOn); a synthetic receptorrecognition element promoter (for example, Stratagene pEGSH vector)which is responsive to a synthetic ecdysone-inducible receptor (forexample, as expressed by the Stratagene pERV3 vector); or anIPTG-inducible promoter (for example, Stratagene pOPI3CAT andpOPRSVI/MCS vectors) which is responsive via a Lac repressor protein.

Alternatively, a pathogen-induced product-detection domain can be a2′,5′-oligoadenylate binding domain, such as, for example, isolated fromhuman Rnase L (NCBI Accession #CAA52920). The 2′,5′-oligoadenylatebinding domain of human RNase L is approximately amino acids 1-335 (B.Dong and R. H. Silverman (1997) Journal of Biological Chemistry 272,22236-22242). Rnase L is expressed in a cell in response to a pathogeninfection and it contains a 2′,5′-oligoadenylate binding domain whichcan be isolated using standard techniques, and used as apathogen-induced product-detection domain in the invention. Furthermore,a single-chain antibody or other molecular structure that binds to2′,5′-oligoadenylate can be used as a pathogen-induced product-detectiondomain.

Further pathogen-induced product-detection domains of the inventioninclude apoptosis-activated molecules, for example, and withoutlimitation, an apoptosis-inducible promoter isolated from one or more ofthe following genes: DIABLO/Smac (P. G. Ekert et al. (2001) J. CellBiology 152, 483-490; S. M. Srinivasula et al. (2001) Nature 410,112-116); Fas/APO-1/CD95 (D. Munsch et al. (2000) J. BiologicalChemistry 275, 3867-3872; M. Mueller et al. (1998) J. Exp. Med. 188,2033-2045); Apaf-1 (A. Fortin et al. (2001) J. Cell Biology 155,207-216); Bax (E. C. Thomborrow and J. J. Manfredi (2001) J. BiologicalChemistry 276, 15598-15608); or other genes whose expression is inducedin apoptosis, as will be appreciated by one of skill in the art. Anotherexample of an apoptosis-inducible promoter is thep53-binding-site-containing promoter of the Stratagene PathDetect® p53vector (Stratagene #219083).

Still other pathogen-induced product-detection domains of the inventioninclude promoters that are activated during an unfolded-protein responseor endoplasmic reticulum-associated protein degradation responses, forexample and without limitation, a suitable promoter containing anendoplasmic reticulum stress response element (ERSE: C. Patil and P.Walter (2001) Current Opinion in Cell Biology 13, 349-356; K. Lee et al.(2002) Genes & Development 16, 452-466; S. Oyadomari et al. (2002)Apoptosis 7, 335-345), ATF6-binding motif (K. Lee et al. (2002) Genes &Development 16, 452-466), or amino-acid response element (AARE: T. Okadaet al. (2002) Biochem. J. 366, 585-594), or a promoter from a gene whoseexpression is induced during unfolded-protein responses or endoplasmicreticulum-associated protein degradation responses, as will beappreciated by one of skill in the art.

Other pathogen-induced product-detection domains of the inventioninclude promoters that are activated during stress responses, forexample and without limitation, a promoter containing a heat shockelement (HSE: S. Ahn et al. (2001) Genes & Development 15, 2134-2145; A.Mathew et al. (2001) Mol. Cell. Biol. 21, 7163-7171), a promoter fromhsp70 or hsp90 genes, or a promoter from another gene whose expressionis induced during stress responses, as will be appreciated by one ofskill in the art.

Still other pathogen-induced product-detection domains of the inventioninclude promoters that are activated during inflammatory responses, forexample and without limitation, a promoter containing an NF-kappa-Bbinding site (F. E. Chen and G. Ghosh (1999) Oncogene 18, 6845-6852; H.L. Pahl (1999) Oncogene 18, 6853-6866), the NF-kappa-B-induciblepromoter of the Stratagene PathDetect® NF-kappaB vector (Stratagene#219077), or a promoter from another gene whose expression is inducedduring inflammatory responses, as will be appreciated by one of skill inthe art.

Other pathogen-induced product-detection domains can be isolated frommolecules that are activated or inhibited during apoptosis or otherforms of pathogen-triggered cell death (A. Muller and T. Rudel (2001)Int. J. Med. Microbiol. 291, 197-207; C. A. Benedict et al. (2002)Nature Immunology 3, 1013-1018; V. T. Heussler et al. (2001)International Journal for Parasitology 31, 1166-1176; L.-Y. Gao and Y.A. Kwaik (2000) Microbes and Infection 2, 1705-1719; L.-Y. Gao and Y. A.Kwaik (2000) Trends Microbiol. 8, 306-313; K. C. Zimmermann et al.(2001) Pharmacology & Therapeutics 92, 57-70; H. R. Stennicke and G. S.Salvesen (2000) Biochimica et Biophysica Acta 1477, 299-306; S. Nagata(1997) Cell 88, 355-365; Z. Song & H. Steller (1999) Trends Cell Biol.9, M49-52), for example and without limitation: p53 (Homo sapiens,#AAF36354 through AAF36382; Mus musculus, #AAC05704, AAD39535, AAF43275,AAF43276, AAK53397); Bax (Homo sapiens, #NM_(—)004324); Bid (Homosapiens, #NM_(—)001196); Bcl-2 (K. C. Zimmermann et al. (2001)Pharmacology & Therapeutics 92, 57-70); inhibitor of apoptosis proteins(IAPs: H. R. Stennicke et al. (2002) TRENDS in Biochemical Sciences 27,94-101; S. M. Srinivasula et al. (2001) Nature 410, 112-116);mitochondrial cytochrome c (K. C. Zimmermann et al. (2001) Pharmacology& Therapeutics 92, 57-70; S. B. Bratton et al. (2001) EMBO Journal 20,998-1009); apoptotic protease activating factor 1 (Apaf-1: Homo sapiens,#NM_(—)013229, NM_(—)001160; Mus musculus, #NP_(—)033814); Fas ligand(Homo sapiens, #D38122; Mus musculus U58995); Fas/CD95 (Homo sapiens,#AAC16236, AAC16237; Mus musculus, #AAG02410); tumor necrosis factoralpha (TNF-α: Homo sapiens, #CAA01558, CAB63904, CAB63905; Mus musculus,#CAA68530); TNF receptors (Homo sapiens, #NP_(—)001056; V. Baud and M.Karin (2001) TRENDS in Cell Biology 11, 372-377; U. Sartorius et al.(2001) Chembiochem 2, 20-29); FLICE-activated death domain (FADD: Homosapiens, #U24231; Mus musculus, #NM_(—)010175); TRADD (Homo sapiens,#NP_(—)003780, CAC38018); perforin (Homo sapiens, #CAA01809,NP_(—)005032; Mus musculus, #CAA42731, CAA35721, AAB01574); granzyme B(Homo sapiens, #AAH30195, NP_(—)004122; Mus musculus, #AAH02085,NP_(—)038570); Smac/DIABLO (Homo sapiens, #NM_(—)019887); caspases(including but not restricted to Caspase 1, Homo sapiens, #NM_(—)001223;Caspase 2, Homo sapiens, #NM_(—)032982, NM_(—)001224, NM_(—)032983, andNM_(—)032984; Caspase 3, Homo sapiens, #U26943; Caspase 4, Homo sapiens,#AAH17839; Caspase 5, Homo sapiens, #NP_(—)004338; Caspase 6, Homosapiens, #NM_(—)001226 and NM_(—)032992; Caspase 7, Homo sapiens,#XM_(—)053352; Caspase 8, Homo sapiens, #NM_(—)001228; Caspase 9, Homosapiens, #AB019197; Caspase 10, Homo sapiens, #XP_(—)027991; Caspase 13,Homo sapiens, #AAC28380; Caspase 14, Homo sapiens, #NP_(—)036246;Caspase 1, Mus musculus, #BC008152; Caspase 2, Mus musculus,#NM_(—)007610; Caspase 3, Mus musculus, #NM_(—)009810; Caspase 6, Musmusculus, #BC002022; Caspase 7, Mus musculus, #BC005428; Caspase 8, Musmusculus, #BC006737; Caspase 9, Mus musculus, #NM_(—)015733; Caspase 11,Mus musculus, #NM_(—)007609; Caspase 12, Mus musculus, #NM_(—)009808;Caspase 14, Mus musculus, #AF092997; and CED-3 caspase, Caenorhabditiselegans, #AF210702); calpains (T. Lu et al., (2002) Biochimica etBiophysica Acta 1590, 16-26); caspase-activated DNase (CAD: Homosapiens, #AB013918; Mus musculus, #AB009377); or inhibitor ofcaspase-activated DNase (ICAD: Mus musculus, #AB009375, AB009376). Apathogen-induced product-detection domain can also be isolated from amolecule that binds to, is activated by, or is inhibited by naturalapoptosis or cell death signaling molecules such as those listed supra.

Other pathogen-detection or pathogen-induced product-detection domainscan be isolated from molecules that are activated stimulated orinhibited during interferon-related or cytokine-related responses (T.Kisseleva et al. (2002) Gene 285, 1-24; A. Garcia-Sastre (2002) Microbesand Infection 4, 647-655; C. E. Samuel (2001) Clinical MicrobiologyReviews 14, 778-809; S. Landolfo et al. (1995) Pharmacol. Ther. 65,415-442), for example and without limitation: interferon-alpha (Homosapiens, #NM_(—)002169, NM_(—)021002, J00207; Mus musculus,#NM_(—)010502, NM_(—)010503, NM_(—)010507, NM_(—)008333, M68944,M13710); interferon-beta (Homo sapiens, #M25460, NM_(—)002176; Musmusculus, #NM_(—)010510); interferon-gamma (Homo sapiens, #NM_(—)000619,J00219; Mus musculus, #M28621); interferon-delta; interferon-tau;interferon-omega (Homo sapiens, #NM_(—)002177); interleukin 1 (IL-1:Homo sapiens, #NM_(—)000575, NM_(—)012275, NM_(—)019618, NM_(—)000576,NM_(—)014439; Mus musculus, #NM_(—)019450, NM_(—)019451, AF230378);interleukin 2 (IL-2: Homo sapiens, #NM_(—)000586); interleukin 3 (IL-3:Homo sapiens, #NM_(—)000588; Mus musculus, #A02046); interleukin 4(IL-4: Homo sapiens, #NM_(—)000589, NM_(—)172348; Mus musculus,#NM_(—)021283); interleukin 5 (IL-5: Homo sapiens, #NM_(—)000879; Musmusculus, #NM_(—)010558); interleukin 6 (IL-6: Homo sapiens,#NM_(—)000600; Mus musculus, #NM_(—)031168); interleukin 7 (IL-7: Homosapiens, #NM_(—)000880, AH006906; Mus musculus, #NM_(—)008371);interleukin 9 (IL-9: Homo sapiens, #NM_(—)000590); interleukin 12(IL-12: Homo sapiens, #NM_(—)000882, NM_(—)002187; Mus musculus,#NM_(—)008351, NM_(—)008352); interleukin 15 (IL-15: Homo sapiens,#NM_(—)172174, NM_(—)172175, NM_(—)000585; Mus musculus, #NM_(—)008357);cytokine receptors and related signaling molecules (W. E. Paul (ed.),Fundamental immunology (4th ed., Lippincott-Raven, Philadelphia, 1999),Chapters 21 and 22); interferon type I receptor subunit 1 (IFNAR1: Homosapiens, #NM_(—)000629; Mus musculus, #NM_(—)010508); interferon type Ireceptor subunit 2 (IFNAR2: Homo sapiens, #NM_(—)000874; Mus musculus,#NM_(—)010509); janus kinase 1 (JAK1: Homo sapiens, #NP_(—)002218; Musmusculus, #NP_(—)666257); janus kinase 2 (JAK2: Homo sapiens, #AAC23653,AAC23982, NP_(—)004963; Mus musculus, #NP_(—)032439, AAN62560); JAK3;Tyk2; signal transducer and activator of transcription 1 (STAT1: Homosapiens, #NM_(—)007315, NM_(—)139266; Mus musculus, #U06924); signaltransducer and activator of transcription 2 (STAT2: Homo sapiens,#NM_(—)005419; Mus musculus, AF206162); STAT3; STAT4; STAT5; STAT6;IRF9/interferon-stimulated gene factor 3 gamma (ISGF3 gamma: Homosapiens, #Q00978, NM_(—)006084; Mus musculus, #NM_(—)008394) interferonregulatory factor 1 (IRF1: Homo sapiens, #NM_(—)002198, P10914; Musmusculus, #NM_(—)008390); interferon regulatory factor 3 (IRF3: Homosapiens, #NM_(—)001571, Z56281; Mus musculus, #NM_(—)016849, U75839,U75840); interferon regulatory factor 5 (IRF5: Homo sapiens, #Q13568,U51127; Mus musculus, #AAB81997, NP_(—)036187); interferon regulatoryfactor 6 (IRF6: Homo sapiens, #AF027292, NM_(—)006147; Mus musculus,#U73029); interferon regulatory factor 7 (IRF7: Homo sapiens, #U53830,U53831, U53832, AF076494, U73036; Mus musculus, #NM_(—)016850, U73037);IRF8; protein kinase R (PKR: Homo sapiens, #AAC50768; Mus musculus,#Q03963; S. Nanduri et al. (1998) EMBO J. 17, 5458-5465); eukaryotictranslation initiation factor 2 alpha (eIF-2alpha: Homo sapiens,#NP_(—)004085); p58 (Homo sapiens, #NP_(—)006251); 2′,5′-oligoadenylatesynthetases (Homo sapiens forms including #P00973, P29728, AAD28543; Musmusculus forms including P11928; S. Y. Desai et al. (1995) J. Biol.Chem. 270, 3454-3461); 2′,5′-oligoadenylate (C. E. Samuel (2001)Clinical Microbiology Reviews 14, 778-809); RNase L (Homo sapiens,#CAA52920); promyelocytic leukemia protein (PML: W. V. Bonilla et al.(2002) Journal of Virology 76, 3810-3818); p56 or related proteins (J.Guo et al. (2000) EMBO Journal 19, 6891-6899; G. C. Sen (2000) Seminarsin Cancer Biology 10, 93-101); p200 or related proteins (G. C. Sen(2000) Seminars in Cancer Biology 10, 93-101); ADAR1 (Homo sapiens,#U18121; Mus musculus, #NP_(—)062629); Mx1 (Homo sapiens,#NM_(—)002462); or Mx2 (Homo sapiens, #NM_(—)002463). A pathogen-inducedproduct-detection domain can also be isolated from a molecule that bindsto, is activated by, or is inhibited by naturalinterferon-response-related signaling or cytokine response-relatedmolecules such as those listed supra.

Other pathogen-detection domains or pathogen-induced product-detectiondomains can be isolated from toll-like receptors, their accessorymolecules, or molecules that they activate directly or indirectly, (S.Akira (2003) Current Opinion in Immunology 15, 5-11; T. Vasselon and P.A. Detmers (2002) Infection and Immunity 70, 1033-1041; C. A. JanewayJr. and R. Medzhitov (2002) Annu. Rev. Immunol. 20, 197-216), includingfor example and without limitation: toll-like receptor 1, Homo sapiens(NCBI Accession #NP_(—)003254, AAC34137); toll-like receptor 2, Homosapiens (NCBI Accession #AAH33756, AAM23001, AAC34133); toll-likereceptor 3, Homo sapiens (NCBI Accession #AAC34134, NP_(—)003256);toll-like receptor 4, Homo sapiens (NCBI Accession #AAC34135, AAF89753,AAF07823, AAF05316); toll-like receptor 5, Homo sapiens (NCBI Accession#AAC34136, BAB43955); toll-like receptor 6, Homo sapiens (NCBI Accession#NP_(—)006059, BAA78631); toll-like receptor 7, Homo sapiens (NCBIAccession #AAF60188, AAF78035, NP_(—)057646, AAH33651); toll-likereceptor 8, Homo sapiens (NCBI Accession #AAF64061, AAF78036); toll-likereceptor 9 Homo sapiens (NCBI Accession # AAG01734, AAG01735, AAG01736,BAB19259); toll-like receptor 10, Homo sapiens (NCBI Accession#AAK26744, NP_(—)112218); CD14, Homo sapiens (NCBI Accession #AAH10507,AAL02401, CAD36116); MD-2, Homo sapiens (NCBI Accession #NP_(—)056179,BAA78717, AAH20690); MD-1, Homo sapiens (NCBI Accession #AAC98152,NP_(—)004262); RP105, Homo sapiens (NCBI Accession #BAA12019); toll/IL-1receptor domain containing adaptor protein (TIRAP), Homo sapiens (NCBIAccession #NP_(—)683708, NP_(—)443119, AAL05627); MyD88, Homo sapiens(NCBI Accession #AAB49967, AAC50954); IL-IR activated kinase 4 (IRAK-4),Homo sapiens (NCBI Accession #CAC60090); TNF-receptor-associated factor6 (TRAF6), Homo sapiens (NCBI Accession #NP_(—)665802, NP_(—)004611);toll-like receptor 1, Mus musculus (NCBI Accession #AAG35062, AAG37302,NP_(—)109607); toll-like receptor 2, Mus musculus (NCBI Accession#AAD46481, AAF04277, AAD49335, NP_(—)036035, AAF28345); toll-likereceptor 3, Mus musculus (NCBI Accession #AAK26117, AAL27007,NP_(—)569054); toll-like receptor 4, Mus musculus (NCBI Accession#AAD29272, AAF04278, AAF05317, NP_(—)067272, AAH29856); toll-likereceptor 5, Mus musculus (NCBI Accession #AAF65625, NP_(—)058624);toll-like receptor 6, Mus musculus (NCBI Accession #BAA78632, AAG38563,NP_(—)035734); toll-like receptor 7, Mus musculus (NCBI Accession#AAK62676, NP_(—)573474, AAL73191, AAL73192); toll-like receptor 8, Musmusculus (NCBI Accession #NP_(—)573475, AAK62677); toll-like receptor 9,Mus musculus (NCBI Accession #BAB19260, AAK29625, AAK28488,NP_(—)112455); CD14, Mus musculus (NCBI Accession #CAA32166, BAB68578,NP_(—)033971); MD-2, Mus musculus (NCBI Accession #BAA93619); MD-1, Musmusculus (NCBI Accession #BAA32399); RP105, Mus musculus (NCBI Accession#BAA07043); toll/IL-1 receptor domain containing adaptor protein(TIRAP), Mus musculus (NCBI Accession #AAL05628, NP_(—)473437); MyD88,Mus musculus (NCBI Accession #AAC53013); IL-IR activated kinase 4(IRAK-4), Mus musculus (NCBI Accession #AAM15773, NP_(—)084202); andTNF-receptor-associated factor 6 (TRAF6), Mus musculus (NCBI Accession#BAA12705, NP_(—)033450). A pathogen-induced product-detection domaincan also be isolated from a molecule that binds to, is activated by, oris inhibited by toll-like-receptor-pathway-related molecules.

Still other pathogen-detection domains or pathogen-inducedproduct-detection domains can be isolated from nucleotide-bindingoligomerization domain (NOD) proteins, or nucleotide-binding-domain(NBD)proteins, or nucleotide-binding-site (NBS)) proteins, or moleculesthat they activate directly or indirectly, (N. Inohara et al. (2002)Current Opinion in Microbiology 5, 76-80; S. E. Girardin et al. (2002)TRENDS in Microbiology 10, 193-199; J. A. Harton et al. (2002) Journalof Immunology 169, 4088-4093; N. Inohara et al. (2000) Journal ofBiological Chemistry 275, 27823-27831), including but not limitedto:Nod1/CARD4 (Homo sapiens, #AAD28350, AAD43922; N. Inohara et al.(1999) Journal of Biological Chemistry 274, 14560-14567); Nod2, (Homosapiens, #AAG33677, AAK70863, AAK70865, AAK70866, AAK70867, AAK70868; Y.Ogura et al. (2001) Journal of Biological Chemistry 276, 4812-4818; N.Inohara et al. (2003) Journal of Biological Chemistry, PMID: 12514169);Ipaf-1/CLAN/CARD12 (Homo sapiens, #NM-021209, AY035391; J.-L. Poyet etal. (2001) Journal of Biological Chemistry 276, 28309-28313); CIITA(Homo sapiens, #AY084054, AY084055, AF410154, NM_(—)000246, X74301; M.W. Linhoff et al. (2001) Molecular and Cellular Biology 21, 3001-3011;A. Muhlethaler-Mottet et al. (1997) EMBO Journal 16, 2851-2860); NAIP(Homo sapiens, #U21912, U19251); Defcap/NAC/NALP1/CARD7 (Homo sapiens,#NM_(—)033004, NM_(—)033005, NM_(—)033006, NM_(—)033007, NM_(—)014922);NBS1/NALP2 (Homo sapiens, #AF310106, NM_(—)017852); cryopyrin/CIAS1(Homo sapiens, #AF410477, AF427617, AH01140, NM_(—)004895); RIP (Homosapiens, #U50062; S. Grimm et al. (1996) Proc. Natl. Acad. Sci. USA 93,10923-10927; H. Hsu et al. (1996) Immunity 4, 387-396);Rip2/RICK/CARDIAK (Homo sapiens, #AF064824, AF078530; N. Inohara et al.(1998) Journal of Biological Chemistry 273, 18675; M. Thome et al.(1998) Current Biology 8, 885-888); and PKK (A. Muto et al. (2002)Journal of Biological Chemistry 277, 31871-31876). A pathogen-inducedproduct-detection domain can also be isolated from a molecule that bindsto, is activated by, or is inhibited by NOD protein pathway-relatedmolecules.

Other pathogen-detection domains or pathogen-induced product-detectiondomains can also be isolated from pentraxins or molecules that theyactivate directly or indirectly, (H. Gewurz et al. (1995) CurrentOpinion in Immunology 7, 54-64), including, but not limited to,C-reactive protein (CRP), Homo sapiens (NCBI Accession #1GNHA, 1GNHB,1GNHC, 1GNHD, 1GNHE, 1GNHF, 1GNHG, 1GNHH, 1GNHI, 1GNHJ); C-reactiveprotein (CRP), Mus musculus (NCBI Accession #CAA31928, NP 031794); serumamyloid P component (SAP), Homo sapiens (NCBI Accession #1SACA, 1SACB,1SACC, 1SACD, 1SACE); and serum amyloid P component (SAP), Mus musculus(NCBI Accession #NP_(—)035448, CAA34774). A pathogen-inducedproduct-detection domain can also be isolated from a molecule that bindsto, is activated by, or is inhibited by pentraxin pathway-relatedmolecules.

Other pathogen-detection domains or pathogen-induced product-detectiondomains can be isolated from collectins or molecules that they activatedirectly or indirectly, (M. Gadjeva et al. (2001) Current Opinion inImmunology 13, 74-78; U. L. Holmskov (2000) APMIS Suppl. 100, 1-59),including for example and without limitation, mannan/mannose bindinglectin (MBL), Homo sapiens (NCBI Accession #AAK52907, CAB56120,CAB56044); mannan/mannose binding lectin (MBL), Mus musculus (NCBIAccession #NP_(—)034905, NP_(—)034906); MBL-associated serine protease 1(MASP1), Homo sapiens (NCBI Accession #NP_(—)001870, NP_(—)624302);MBL-associated serine protease 2 (MASP2), Homo sapiens (NCBI Accession#NP_(—)006601, NP_(—)631947, AAG50274, BAA85659); MBL-associated serineprotease 1 (MASP1), Mus musculus (NCBI Accession #XP_(—)193834);MBL-associated serine protease 2 (MASP2), Mus musculus (NCBI Accession#BAA34674, CAB65247, CAB65250); MBL-associated serine protease 3(MASP3), Mus musculus (NCBI Accession #BAB69688); surfactant protein A(SP-A), Homo sapiens (NCBI Accession #NP_(—)005402, NP_(—)008857);surfactant protein D (SP-D), Homo sapiens (NCBI Accession #CAA46152,NP_(—)003010); surfactant protein D (SP-D), Mus musculus (NCBI Accession#AAF15277); surfactant protein D (SP-D), Bos taurus (NCBI Accession#CAA53510, S33603); conglutinin, Bos taurus (NCBI Accession #CAA50665,BAA03170); collectin-43 (CL-43), Bos taurus (NCBI Accession #CAA53511,P42916, A53570); collectin-L1, Mus musculus (NCBI Accession #BAC53954);and collectin placenta 1 (CL-P1), Homo sapiens (NCBI Accession#AB005145). A pathogen-induced product-detection domain can also beisolated from a molecule that binds to, is activated by, or is inhibitedby collectin pathway-related molecules.

Still other pathogen-detection domains or pathogen-inducedproduct-detection domains can be isolated from mannose receptors ormolecules that they activate directly or indirectly, (L. East and C. M.Isacke (2002) Biochimica et Biophysica Acta 1572, 364-386; S. Zamze etal. (2002) Journal of Biological Chemistry 277, 41613-41623), includingfor example and without limitation, mannose receptor (MR), Homosapiens(NCBI Accession #NM_(—)002438); and mannose receptor (MR), Musmusculus (NCBI Accession #CAA78028, NP_(—)032651, NP_(—)032652). Apathogen-induced product-detection domain can also be isolated from amolecule that binds to, is activated by, or is inhibited by mannosereceptor pathway-related molecules.

Other pathogen-detection domains or pathogen-induced product-detectiondomains can also be isolated from scavenger receptors or molecules thatthey activate directly or indirectly, (L. Peiser et al. (2002) CurrentOpinion in Immunology 14, 123-128; A. Brannstrom et al. (2002)Biochemical and Biophysical Research Communications 290, 1462-1469),including for example and without limitation, scavenger receptor A I(SR-A I), Homo sapiens (NCBI Accession #D90187); scavenger receptor A II(SR-A II), Homo sapiens (NCBI Accession #D90188); scavenger receptor A I(SR-A I), Mus musculus (NCBI Accession #L04274); scavenger receptor A II(SR-A II), Mus musculus (NCBI Accession #L04275); macrophage receptorwith collagenous structure (MARCO), Homo sapiens (NCBI Accession#NP_(—)006761); macrophage receptor with collagenous structure (MARCO),Mus musculus (NCBI Accession #NP_(—)034896); scavenger receptor withC-type lectin I (SR-CL I), Homo sapiens (NCBI Accession #BAB39147);scavenger receptor with C-type lectin II (SR-CL II), Homo sapiens (NCBIAccession #BAB39148); and scavenger receptor with C-type lectin (SR-CL),Mus musculus (NCBI Accession #BAB82497). A pathogen-inducedproduct-detection domain can also be isolated from a molecule that bindsto, is activated by, or is inhibited byscavenger-receptor-pathway-related molecules.

Other pathogen-detection domains or pathogen-induced product-detectiondomains can be isolated from molecules that initiate, signal, or detectimmune-related responses (W. E. Paul (ed.), Fundamental Immunology (4thed., Lippincott-Raven, Philadelphia, 1999); M. T. M. Vossen et al.(2002) Immunogenetics 54, 527-542), for example and without limitationthe following molecules or DNA or RNA encoding them: MHC Class I; MHCClass II; antibodies; single-chain antibodies; T cell receptors; Fcreceptors; NK cell activation receptors (including but not limited toNKp46, Ly49H, and NKG2D; A. Diefenbach and D. H. Raulet (2003) CurrentOpinion in Immunology 15, 37-44; A. R. French and W. M. Yokoyama (2003)Current Opinion in Immunology 15, 45-51); NK cell inhibitory receptors;receptor-associated tyrosine kinases; or phospholipase C. Apathogen-detection domain or pathogen-induced product-detection domaincan also be isolated from a molecule that binds to, is activated by, oris inhibited by immune-response-pathway-related molecules.

Other pathogen-detection domains or pathogen-induced product-detectiondomains can be isolated from molecules that are activated or inhibitedduring unfolded protein response-related or endoplasmicreticulum-associated protein degradation-related responses (C. Patil andP. Walter (2001) Current Opinion in Cell Biology 13, 349-356; K. Lee etal. (2002) Genes & Development 16, 452-466; S. Oyadomari et al. (2002)Apoptosis 7, 335-345), for example and without limitation:BiP/GRP78/SHPA5 (Homo sapiens, #AJ271729, AF216292, X87949,NM_(—)005347; Mus musculus, #NM_(—)022310); PKR-like endoplasmicreticulum kinase (PERK: Homo sapiens, #NP_(—)004827; Mus musculus,#AAD03337, NP_(—)034251); IRE1 alpha (Homo sapiens, #AF059198; Musmusculus, #AB031332, AF071777); IRE1 beta (Homo sapiens, #AB047079); RNAfor IRE1 alpha or IRE1 beta (W. Tirasophon et al. (2000) Genes &Development 14, 2725-2736); p58 (Homo sapiens, #NP_(—)006251; W. Yan etal. (2002) Proc. Natl. Acad. Sci. USA 99, 15920-15925); activatingtranscription factor 4 (ATF4: Homo sapiens, #NM_(—)001675; Mus musculus,#NM_(—)009716); activating transcription factor 6 alpha or beta (ATF6alpha or beta: Homo sapiens, #NM_(—)007348, AF005887, AB015856; Musmusculus, #XM_(—)129579); X-box binding protein 1 (XBP1: Homo sapiens,#AB076383, AB076384; Mus musculus, #AF443192, AF027963, NM_(—)013842);XBP1 RNA (K. Lee et al. (2002) Genes & Development 16, 452-466; H.Yoshida et al. (2001) Cell 107, 881-891); CHOP-10/GADD153/DDIT3 (Homosapiens, #NM_(—)004083; Mus musculus, #X67083, NM_(—)007837); site-1protease (S1P: Homo sapiens, #NM_(—)003791; Mus musculus,#NM_(—)019709); site-2 protease (S2P: Homo sapiens, #NM_(—)015884);presenilin-1 (Homo sapiens, #AH004968, AF416717; Mus musculus,#BC030409, NM_(—)008943, AF149111); TNF receptor-associated factor 2(TRAF2: Homo sapiens, #NM_(—)021138, NM_(—)145718, Mus musculus,#XM_(—)203851, XM_(—)130119, L35303); cJUN NH2-terminal kinases (JNKs:S. Oyadomari et al. (2002) Apoptosis 7, 335-345); or eukaryotictranslation initiation factor 2 alpha (eIF-2alpha: Homo sapiens,#NP_(—)004085). A pathogen-detection domain or pathogen-inducedproduct-detection domain can also be isolated from a molecule that bindsto, is activated by, or is inhibited by natural unfolded proteinresponse-related or endoplasmic reticulum-associated proteindegradation-related molecules such as those listed supra.

Still other pathogen-induced product-detection domains of the inventioninclude a promoter that is activated or inhibited during anunfolded-protein response orendoplasmic-reticulum-associated-protein-degradation response, forexample and without limitation, an isolated promoter containing anendoplasmic reticulum stress response element (ERSE: C. Patil and P.Walter (2001) Current Opinion in Cell Biology 13, 349-356; K. Lee et al.(2002) Genes & Development 16, 452-466; S. Oyadomari et al. (2002)Apoptosis 7, 335-345), ATF6-binding motif (K. Lee et al. (2002) Genes &Development 16, 452-466), or amino-acid response element (AARE: T. Okadaet al. (2002) Biochem. J. 366, 585-594), or a promoter from a gene whoseexpression is induced or repressed during an unfolded-protein responseor endoplasmic-reticulum-associated-protein-degradation response, aswill be appreciated by one of skill in the art.

Other pathogen-detection domains or pathogen-induced product-detectiondomains can be isolated from molecules that are activated or inhibitedduring a stress or inflammatory response (R. I. Morimoto and M. G.Santoro (1998) Nature Biotech. 16, 833-838; R. I. Morimoto (1998) Genes& Dev. 12, 3788-3796; M. G. Santoro (2000) Biochem. Pharmacol. 59,55-63; A. De Marco et al. (1998) Eur. J. Biochem. 256, 334-341; C. Contiet al. (1999) Antimicrobial Agents and Chemotherapy 43, 822-829; M. G.Santoro (1996) EXS 77, 337-357; E. A. A. Nollen and R. I. Morimoto(2002) Journal of Cell Science 115, 2809-2816; J. Hiscott et al. (2001)J. Clinical Investigation 107, 143-151; E. N. Hatada et al. (2000) Curr.Opin. Immunol. 12, 52-58; T. Wang et al. (2002) Int. Immunopharmacol. 2,1509-1520; X. Li and G. R. Stark (2002) Exp. Hematol. 30, 285-296; Z.Sun and R. Andersson (2002) Shock 18, 99-106; H. L. Pahl (1999) Oncogene18, 6853-6866; F. Mercurio and A. M. Manning Oncogene 18, 6163-6167)),for example and without limitation: heat shock protein 70 or relatedproteins (Hsp70: Homo sapiens, #M11717, M15432, L12723, NM_(—)016299,NM_(—)005346, NM_(—)005345, NM_(—)002155, NM_(—)021979, AF093759; Musmusculus, #XM_(—)207065, XM_(—)128584, XM_(—)128585, XM_(—)110217,NM_(—)015765, NM_(—)010481, NM_(—)008301, M76613); Hsp90 (Homo sapiens,#M16660, NM_(—)005348, NM_(—)007355); Hsp40/Hdj-1 (Homo sapiens,#X62421, NM_(—)006145, NM_(—)005880); Hsc70 (Homo sapiens, #AF352832);Hsp47/CBP-2 (Homo sapiens, #D83174); cdc48 (S. Thoms (2002) FEBS Lett.520, 107-110); Bip/GRP78; Hsp60 (Homo sapiens, #NM_(—)002156); Hsp100(Homo sapiens, #NM_(—)006660); Alpha-A-crystallin (Homo sapiens,#NM_(—)000394); Alpha-B-crystallin (Homo sapiens, #NM_(—)001885);Hsp27-1 (Homo sapiens, #NM_(—)001540); Hsp27-2 (Homo sapiens,#XM_(—)012054); heat shock factor 1 (HSF1: Homo sapiens, #NM_(—)005526,M64673; Mus musculus, #XM_(—)128055, X61753, Z49206; A. Mathew et al.(2001) Mol. Cell. Biol. 21, 7163-7171; L. Pirkkala et al. (2001) FASEBJ. 15, 1118-1131); heat shock factor 2 (HSF2: Homo sapiens,#NM_(—)004506; Mus musculus, #X61754, AH007205, NM_(—)008297); heatshock factor 3 (HSF3: L. Pirkkala et al. (2001) FASEB J. 15,1.118-1131); heat shock factor 4 (HSF4: Homo sapiens, #NM_(—)001538,D87673, AB029348; Mus musculus, #AF160965, AF160966, AB029349,AB029350); heat shock factor binding protein 1 (HSBP1: Homo sapiens,#NM_(—)001537, BC007515, AF068754); heat shock factor 2 binding protein(HSF2BP: Homo sapiens, #NM_(—)007031); RelA/p65 (Homo sapiens,#NM_(—)021975, Z22948, L19067; Mus musculus, #NM_(—)009045, AF199371);RelB (Homo sapiens, #NM_(—)006509; Mus musculus, #NM_(—)009046, M83380);c-Rel (Homo sapiens, #X75042, NM_(—)002908; Mus musculus, #NM_(—)009044,X15842); p50/p105/NF-kappa B 1 (Homo sapiens, #NM_(—)003998, S76638,AF213884, AH009144; Mus musculus, #NM_(—)008689, AK052726, M57999);p52/p100/NF-kappa B 2 (Homo sapiens, #NM_(—)002502; Mus musculus,#AF155372, AF155373, NM_(—)019408); inhibitors of kappa B (I kappa B:Homo sapiens, #AY033600, NM_(—)020529; S. Ghosh and M. Karin (2002) Cell109, S81-S96); IKK1/I kappa B kinase alpha (IKK alpha: Homo sapiens, #AF009225, AF080157); IKK2/I kappa B kinase beta (IKK beta: Homo sapiens,#AF080158; Mus musculus, #AF026524, AF088910); NEMO/I kappa B kinasegamma (IKK gamma: Homo sapiens, #AF261086, AF091453; Mus musculus,#AF069542). A pathogen detection domain or pathogen-inducedproduct-detection domain can also be isolated from a molecule that bindsto, is activated by, or is inhibited by a stress response-related orinflammatory response-related molecule such as those listed supra.

Still other pathogen-induced product-detection domains of the inventioninclude promoters that are activated or inhibited during stress orinflammatory responses, for example and without limitation, a promotercontaining a heat shock element (HSE: S. Ahn et al. (2001) Genes &Development 15, 2134-2145; A. Mathew et al. (2001) Mol. Cell. Biol. 21,7163-7171) or NF-kappa-B binding site (F. E. Chen and G. Ghosh (1999)Oncogene 18, 6845-6852; H. L. Pahl (1999) Oncogene 18, 6853-6866), apromoter from hsp70 or hsp90 genes, or a promoter from another genewhose expression is induced or repressed during stress or inflammatoryresponses as will be appreciated by one of skill in the art.

Other pathogen-detection domains or pathogen-induced product-detectiondomains can be isolated from complement pathway-related molecules (W. E.Paul (ed.), Fundamental Immunology (4th ed., Lippincott-Raven,Philadelphia, 1999), Chapter 29; M. K. Pangburn et al. (2000) Journal ofImmunology 164, 4742-4751), for example and without limitation: C3alpha, C3 beta, factor B, factor D, properdin, C1q, C1r, C1s, C4, C2,C5, C6, C7, C8, C9, factor I, factor H, C1-INH, C4 bp, S protein,clusterin, carboxypeptidase N, FHL-1, FHR-1, FHR-2, FHR-3, FHR-4, CR1,or DAF. A pathogen detection domain or pathogen-inducedproduct-detection domain can also be isolated from a molecule that bindsto, is activated by, or is inhibited by natural complementpathway-related molecules such as those listed supra.

Effector domains of this invention can mediate, either directly orindirectly, a wide range of effector functions. These include, forexample and without limitation, one or more of the following responses:(1) an interferon response; (2) an apoptosis response; (3) stressresponse; (4) an enhanced immune response; (5) the expression of adouble-stranded RNase; (6) inhibition of nuclear localization oftargets; (7) inhibition of endosome function or activity; and otheranti-pathogen responses.

As used herein, the effector domain is a region of the molecule thatincludes at least the minimal region necessary to perform the describedeffector function of the domain. The effector domain can also beencompassed within a larger or smaller region or structure, but it stillretains the effector function of the domain.

More particularly, an effector domain as used herein is a molecule thatbinds to or acts on one or more of the following: a pathogen (forexample: a peptide containing amino acids 119-136 of hamster prionprotein that binds to and inhibits a pathogenic prion); a pathogencomponent (for example, a molecule that binds to a viral late domainmotif, thereby inhibiting viral budding or release, as describedherein); a molecule produced or induced by a pathogen (for example, anRNase III that degrades dsRNA produced in a virus-infected cell, asdescribed herein); a natural anti-pathogen molecule (for example, amolecule that activates caspases in an infected cell, thereby killingsaid cell and preventing further spread of the infection); a componentthat is naturally occurring in a cell or organism and that directly orindirectly activates or inhibits an anti-pathogen molecule, or acomponent that is naturally occurring within a cell or organism and thataids a pathogen or pathogenic effect (for example, a molecule that bindsto vacuolar ATPase and inhibits acidification of endosomes in a cell,thereby inhibiting infection of the cell by a virus, as describedherein). By binding or acting as described supra and herein, theeffector domain exerts an anti-pathogen effect, for example, and withoutlimitation, by performing one or more of the following functions:inhibiting infection of a cell or organism by a pathogen; inhibitingreplication of a pathogen; destroying or neutralizing a pathogen; ormaking a pathogen more vulnerable to other therapeutic anti-pathogenmolecules or to natural anti-pathogen molecules. An effector domain canbelong to multiple categories described herein.

Effector domains can be isolated from naturally-occurring molecules thatnormally mediate the function of an effector domain as described herein,such as a cellular protein. Effector domains can be isolated from a widerange of known cellular proteins from a number of different organisms,including for example, humans, non-human primates, rodents, plants,Drosophila, yeast, bacteria and the like, as will be appreciated by oneof skill in the art. The effector domain can also besynthetically-derived, such as by chemically modifying anaturally-occurring molecule, or otherwise manipulating anaturally-occurring molecule to enhance, optimize, or modify theeffector domain, using standard techniques known to those of skill inthe art. Alternatively, an effector domain can be a synthetic productsuch as a small molecule or a peptidomimetic. Furthermore, an effectordomain can be an antibody (including, for example, antibody fragments,such as Fab, Fab′, F(ab′)₂, and fragments including either a V_(L) orV_(H) domain, single chain antibodies, bi-specific, chimeric orhumanized antibodies), that performs the function of an effector domain.

Effector domains can be isolated from molecules that execute, stimulate,or inhibit apoptosis or other forms of cell death (A. Muller and T.Rudel (2001) Int. J. Med. Microbiol. 291, 197-207; C. A. Benedict et al.(2002) Nature Immunology 3, 1013-1018; V. T. Heussler et al. (2001)International Journal for Parasitology 31, 1166-1176; L.-Y. Gao and Y.A. Kwaik (2000) Microbes and Infection 2, 1705-1719; L.-Y. Gao and Y. A.Kwaik (2000) Trends Microbiol. 8, 306-313; K. C. Zimmermann et al.(2001) Pharmacology & Therapeutics 92, 57-70; H. R. Stennicke and G. S.Salvesen (2000) Biochimica et Biophysica Acta 1477, 299-306; S. Nagata(1997) Cell 88, 355-365; Z. Song & H. Steller (1999) Trends Cell Biol.9, M49-52), for example and without limitation, the following moleculesor DNA or RNA encoding them: p53 (Homo sapiens, #AAF36354 throughAAF36382; Mus musculus, #AAC05704, AAD39535, AAF43275, AAF43276,AAK53397); Bax (Homo sapiens, #NM_(—)004324); Bid (Homo sapiens,#NM_(—)001196); Bcl-2 (K. C. Zimmermann et al. (2001) Pharmacology &Therapeutics 92, 57-70); inhibitor of apoptosis proteins (IAPs: H. R.Stennicke et al. (2002) TRENDS in Biochemical Sciences 27, 94-101; S. M.Srinivasula et al. (2001) Nature 410, 112-116); mitochondrial cytochromec (K. C. Zimmermann et al. (2001) Pharmacology & Therapeutics 92, 57-70;S. B. Bratton et al. (2001) EMBO Journal 20, 998-1009); apoptoticprotease activating factor 1 (Apaf-1: Homo sapiens, #NM_(—)013229,NM_(—)001160; Mus musculus, #NP_(—)033814); Fas ligand (Homo sapiens,#D38122; Mus musculus U58995); Fas/CD95 (Homo sapiens, #AAC16236,AAC16237; Mus musculus, #AAG02410); tumor necrosis factor alpha (TNF-a:Homo sapiens, #CAA01558, CAB63904, CAB63905; Mus musculus, #CAA68530);TNF receptors (Homo sapiens, #NP_(—)001056; V. Baud and M. Karin (2001)TRENDS in Cell Biology 11, 372-377; U. Sartorius et al. (2001)Chembiochem 2, 20-29); FLICE-activated death domain (FADD: Homo sapiens,#U24231; Mus musculus, #NM_(—)010175); TRADD (Homo sapiens,#NP_(—)003780, CAC38018); perforin (Homo sapiens, #CAA01809,NP_(—)005032; Mus musculus, #CAA42731, CAA35721, AAB01574); granzyme B(Homo sapiens, #AAH30195, NP_(—)004122; Mus musculus, #AAH02085,NP_(—)038570); Smac/DIABLO (Homo sapiens, #NM_(—)019887); caspases(including but not restricted to Caspase 1, Homo sapiens, #NM_(—)001223;Caspase 2, Homo sapiens, #NM_(—)032982, NM_(—)001224, NM_(—)032983, andNM_(—)032984; Caspase 3, Homo sapiens, #U26943; Caspase 4, Homo sapiens,#AAH17839; Caspase 5, Homo sapiens, #NP_(—)004338; Caspase 6, Homosapiens, #NM_(—)001226 and NM_(—)032992; Caspase 7, Homo sapiens,#XM_(—)053352; Caspase 8, Homo sapiens, #NM_(—)001228; Caspase 9, Homosapiens, #AB019197; Caspase 10, Homo sapiens, #XP_(—)027991; Caspase 13,Homo sapiens, #AAC28380; Caspase 14, Homo sapiens, #NP_(—)036246;Caspase 1, Mus musculus, #BC008152; Caspase 2, Mus musculus,#NM_(—)007610; Caspase 3, Mus musculus, #NM_(—)009810; Caspase 6, Musmusculus, #BC002022; Caspase 7, Mus musculus, #BC005428; Caspase 8, Musmusculus, #BC006737; Caspase 9, Mus musculus, #NM_(—)015733; Caspase 11,Mus musculus, #NM_(—)007609; Caspase 12, Mus musculus, #NM_(—)009808;Caspase 14, Mus musculus, #AF092997; and CED-3 caspase, Caenorhabditiselegans, #AF210702); calpains (T. Lu et al., (2002) Biochimica etBiophysica Acta 1590, 16-26); caspase-activated DNase (CAD: Homosapiens, #AB013918; Mus musculus, #AB009377); or inhibitor ofcaspase-activated DNase (ICAD: Mus musculus, #AB009375, AB009376). Aneffector domain can also be isolated from a molecule that binds to,stimulates, or inhibits natural apoptosis or cell death signalingmolecules such as those listed supra.

Other effector domains can be isolated from molecules that execute,stimulate, or inhibit interferon-related or cytokine-related responses(T. Kisseleva et al. (2002) Gene 285, 1-24; A. Garcia-Sastre (2002)Microbes and Infection 4, 647-655; C. E. Samuel (2001) ClinicalMicrobiology Reviews 14, 778-809; S. Landolfo et al. (1995) Pharmacol.Ther. 65, 415-442), for example and without limitation, the followingmolecules or DNA or RNA encoding them: interferon-alpha (Homo sapiens,#NM_(—)002169, NM_(—)021002, J00207; Mus musculus, #NM_(—)010502,NM_(—)010503, NM_(—)010507, NM_(—)008333, M68944, M13710);interferon-beta (Homo sapiens, #M25460, NM_(—)002176; Mus musculus,#NM_(—)010510); interferon-gamma (Homo sapiens, #NM_(—)000619, J00219;Mus musculus, #M28621); interferon-delta; interferon-tau;interferon-omega (Homo sapiens, #NM_(—)002177); interleukin 1 (IL-1:Homo sapiens, #NM_(—)000575, NM_(—)012275, NM_(—)019618, NM_(—)000576,NM_(—)014439; Mus musculus, #NM_(—)019450, NM_(—)019451, AF230378);interleukin 2 (IL-2: Homo sapiens, #NM_(—)000586); interleukin 3 (IL-3:Homo sapiens, #NM_(—)000588; Mus musculus, #A02046); interleukin 4(IL-4: Homo sapiens, #NM_(—)000589, NM_(—)172348; Mus musculus,#NM_(—)021283); interleukin 5 (IL-5: Homo sapiens, #NM_(—)000879; Musmusculus, #NM_(—)010558); interleukin 6 (IL-6: Homo sapiens,#NM_(—)000600; Mus musculus, #NM_(—)031168); interleukin 7 (IL-7: Homosapiens, #NM_(—)000880, AH006906; Mus musculus, #NM_(—)008371);interleukin 9 (IL-9: Homo sapiens, #NM_(—)000590); interleukin 12(IL-12: Homo sapiens, #NM_(—)000882, NM_(—)002187; Mus musculus,#NM_(—)008351, NM_(—)008352); interleukin 15 (IL-15: Homo sapiens,#NM_(—)172174, NM_(—)172175, NM_(—)000585; Mus musculus, #NM_(—)008357);cytokine receptors and related signaling molecules (W. E. Paul (ed.),Fundamental Immunology (4th ed., Lippincott-Raven, Philadelphia, 1999),Chapters 21 and 22); interferon type I receptor subunit 1 (IFNAR1: Homosapiens, #NM_(—)000629; Mus musculus, #NM_(—)010508); interferon type Ireceptor subunit 2 (IFNAR2: Homo sapiens, #NM_(—)000874; Mus musculus,#NM_(—)010509); janus kinase 1 (JAK1: Homo sapiens, #NP_(—)002218; Musmusculus, #NP_(—)666257); janus kinase 2 (JAK2: Homo sapiens, #AAC23653,AAC23982, NP_(—)004963; Mus musculus, #NP_(—)032439, AAN62560); JAK3;Tyk2; signal transducer and activator of transcription 1 (STAT1: Homosapiens, #NM_(—)007315, NM_(—)139266; Mus musculus, #U06924); signaltransducer and activator of transcription 2 (STAT2: Homo sapiens,#NM_(—)005419; Mus musculus, AF206162); STAT3; STAT4; STAT5; STAT6;IRF9/interferon-stimulated gene factor 3 gamma (ISGF3 gamma: Homosapiens, #Q00978, NM_(—)006084; Mus musculus, #NM_(—)008394) interferonregulatory factor 1 (IRF1: Homo sapiens, #NM_(—)002198, P10914; Musmusculus, #NM_(—)008390); interferon regulatory factor 3 (IRF3: Homosapiens, #NM_(—)001571, Z56281; Mus musculus, #NM_(—)016849, U75839,U75840); interferon regulatory factor 5 (IRF5: Homo sapiens, #Q13568,U51127; Mus musculus, #AAB81997, NP_(—)036187); interferon regulatoryfactor 6 (IRF6: Homo sapiens, #AF027292, NM_(—)006147; Mus musculus,#U73029); interferon regulatory factor 7 (IRF7: Homo sapiens, #U53830,U53831, U53832, AF076494, U73036; Mus musculus, #NM_(—)016850, U73037);protein kinase R (PKR: Homo sapiens, #AAC50768; Mus musculus, #Q03963;S. Nanduri et al. (1998) EMBO J. 17, 5458-5465); eukaryotic translationinitiation factor 2 alpha (eIF-2alpha: Homo sapiens, #NP_(—)004085); p58(Homo sapiens, #NP_(—)006251); 2′,5′-oligoadenylate synthetases (Homosapiens forms including #P00973, P29728, AAD28543; Mus musculus formsincluding P11928; S. Y. Desai et al. (1995) J. Biol. Chem. 270,3454-3461); 2′,5′-oligoadenylate (C. E. Samuel (2001) ClinicalMicrobiology Reviews 14, 778-809); RNase L (Homo sapiens, #CAA52920);promyelocytic leukemia protein (PML: W. V. Bonilla et al. (2002) Journalof Virology 76, 3810-3818); p56 or related proteins (J. Guo et al.(2000) EMBO Journal 19, 6891-6899; G. C. Sen (2000) Seminars in CancerBiology 10, 93-101); p200 or related proteins (G. C. Sen (2000) Seminarsin Cancer Biology 10, 93-101); ADAR1 (Homo sapiens, #U18121; Musmusculus, #NP_(—)062629); Mx1 (Homo sapiens, #NM_(—)002462); or Mx2(Homo sapiens, #NM_(—)002463). An effector domain can also be isolatedfrom a molecule that binds to, stimulates, or inhibits naturalinterferon-response-related or cytokine-response related molecules suchas those listed supra.

Other effector domains can be isolated from molecules that execute,stimulate, or inhibit stress or inflammatory responses (R. I. Morimotoand M. G. Santoro (1998) Nature Biotech. 16, 833-838; R. I. Morimoto(1998) Genes & Dev. 12, 3788-3796; M. G. Santoro (2000) Biochem.Pharmacol. 59, 55-63; A. De Marco et al. (1998) Eur. J. Biochem. 256,334-341; C. Conti et al. (1999) Antimicrobial Agents and Chemotherapy43, 822-829; M. G. Santoro (1996) EXS 77, 337-357; E. A. A. Nollen andR. I. Morimoto (2002) Journal of Cell Science 115, 2809-2816; J. Hiscottet al. (2001) J. Clinical Investigation 107, 143-151; E. N. Hatada etal. (2000) Curr. Opin. Immunol. 12, 52-58; T. Wang et al. (2002) Int.Immunopharmacol. 2, 1509-1520; X. Li and G. R. Stark (2002) Exp.Hematol. 30, 285-296; Z. Sun and R. Andersson (2002) Shock 18, 99-106;H. L. Pahl (1999) Oncogene 18, 6853-6866; F. Mercurio and A. M. ManningOncogene 18, 6163-6167)), for example and without limitation, thefollowing molecules or DNA or RNA encoding them: heat shock protein 70or related proteins (Hsp70: Homo sapiens, #M11717, M15432, L12723,NM_(—)016299, NM_(—)005346, NM_(—)005345, NM_(—)002155, NM_(—)021979,AF093759; Mus musculus, #XM_(—)207065, XM_(—)128584, XM_(—)128585,XM_(—)110217, NM_(—)015765, NM_(—)010481, NM_(—)008301, M76613); Hsp90(Homo sapiens, #M16660, NM_(—)005348, NM_(—)007355); Hsp40/Hdj-1 (Homosapiens, #X62421, NM_(—)006145, NM_(—)005880); Hsc70 (Homo sapiens,#AF352832); Hsp47/CBP-2 (Homo sapiens, #D83174); cdc48 (S. Thoms (2002)FEBS Lett. 520, 107-110); Bip/GRP78; Hsp60 (Homo sapiens,#NM_(—)002156); Hsp100 (Homo sapiens, #NM_(—)006660); Alpha-A-crystallin(Homo sapiens, #NM_(—)000394); Alpha-B-crystallin (Homo sapiens,#NM_(—)001885); Hsp27-1 (Homo sapiens, #NM_(—)001540); Hsp27-2 (Homosapiens, #XM_(—)012054); heat shock factor 1 (HSF1: Homo sapiens,#NM_(—)005526, M64673; Mus musculus, #XM_(—)128055, X61753, Z49206; A.Mathew et al. (2001) Mol. Cell. Biol. 21, 7163-7171; L. Pirkkala et al.(2001) FASEB J. 15, 1118-1131); heat shock factor 2 (HSF2: Homo sapiens,#NM_(—)004506; Mus musculus, #X61754, AH007205, NM_(—)008297); heatshock factor 3 (HSF3: L. Pirkkala et al. (2001) FASEB J. 15, 1118-1131);heat shock factor 4 (HSF4: Homo sapiens, #NM_(—)001538, D87673,AB029348; Mus musculus, #AF160965, AF160966, AB029349, AB029350); heatshock factor binding protein 1 (HSBP1: Homo sapiens, #NM_(—)001537,BC007515, AF068754); heat shock factor 2 binding protein (HSF2BP: Homosapiens, #NM_(—)007031); RelA/p65 (Homo sapiens, #NM_(—)021975, Z22948,L19067; Mus musculus, #NM_(—)009045, AF199371); RelB (Homo sapiens,#NM_(—)006509; Mus musculus, #NM_(—)009046, M83380); c-Rel (Homosapiens, #X75042, NM_(—)002908; Mus musculus, #NM_(—)009044, X15842);p50/p105/NF-kappa B 1 (Homo sapiens, #NM_(—)003998, S76638, AF213884,AH009144; Mus musculus, #NM_(—)008689, AK052726, M57999);p52/p100/NF-kappa B 2 (Homo sapiens, #NM_(—)002502; Mus musculus,#AF155372, AF155373, NM_(—)019408); inhibitors of kappa B (I kappa B:Homo sapiens, #AY033600, NM_(—)020529; S. Ghosh and M. Karin (2002) Cell109, S81-S96); IKK1/I kappa B kinase alpha (IKK alpha: Homo sapiens, #AF009225, AF080157); IKK2/1 kappa B kinase beta (IKK beta: Homo sapiens,#AF080158; Mus musculus, #AF026524, AF088910); NEMO/I kappa B kinasegamma (IKK gamma: Homo sapiens, #AF261086, AF091453; Mus musculus,#AF069542). An effector domain can also be isolated from a molecule thatbinds to, stimulates, or inhibits natural stress-response-related orinflammatory-response-related molecules such as those listed supra.

Other effector domains can be isolated from molecules that execute,stimulate, or inhibit unfolded protein response-related or endoplasmicreticulum-associated protein degradation-related responses (C. Patil andP. Walter (2001) Current Opinion in Cell Biology 13, 349-356; K. Lee etal. (2002) Genes & Development 16, 452-466; S. Oyadomari et al. (2002)Apoptosis 7, 335-345), for example and without limitation, the followingmolecules or DNA or RNA encoding them: BiP/GRP78/SHPA5 (Homo sapiens,#AJ271729, AF216292, X87949, NM_(—)005347; Mus musculus, #NM_(—)022310);PKR-like endoplasmic reticulum kinase (PERK: Homo sapiens,#NP_(—)004827; Mus musculus, #AAD03337, NP_(—)034251); IRE1 alpha (Homosapiens, #AF059198; Mus musculus, #AB031332, AF071777); IRE1 beta (Homosapiens, #AB047079); RNA for IRE1 alpha or IRE1 beta (W. Tirasophon etal. (2000) Genes & Development 14, 2725-2736); p58 (Homo sapiens,#NP_(—)006251; W. Yan et al. (2002) Proc. Natl. Acad. Sci. USA 99,15920-15925); activating transcription factor 4 (ATF4: Homo sapiens,#NM_(—)001675; Mus musculus, #NM_(—)009716); activating transcriptionfactor 6 alpha or beta (ATF6 alpha or beta: Homo sapiens, #NM_(—)007348,AF005887, AB015856; Mus musculus, #XM_(—)129579); X-box binding protein1 (XBP1: Homo sapiens, #AB076383, AB076384; Mus musculus, #AF443192,AF027963, NM_(—)013842); XBP1 RNA (K. Lee et al. (2002) Genes &Development 16, 452-466; H. Yoshida et al. (2001) Cell 107, 881-891);CHOP-10/GADD153/DDIT3 (Homo sapiens, #NM_(—)004083; Mus musculus,#X67083, NM_(—)007837); site-1 protease (S1P: Homo sapiens,#NM_(—)003791; Mus musculus, #NM_(—)019709); site-2 protease (S2P: Homosapiens, #NM_(—)015884); presenilin-1 (Homo sapiens, #AH004968,AF416717; Mus musculus, #BC030409, NM_(—)008943, AF149111); TNFreceptor-associated factor 2 (TRAF2: Homo sapiens, #NM_(—)021138,NM_(—)145718, Mus musculus, #XM_(—)203851, XM_(—)130119, L35303); cJUNNH2-terminal kinases (JNKs: S. Oyadomari et al. (2002) Apoptosis 7,335-345); or eukaryotic translation initiation factor 2 alpha(eIF-2alpha: Homo sapiens, #NP_(—)004085). An effector domain can alsobe isolated from a molecule that binds to, stimulates, or inhibitsnatural unfolded protein response-related or endoplasmicreticulum-associated protein degradation-related molecules such as thoselisted supra.

An effector domain can be any naturally or non-naturally occurringmolecule that binds to a pathogen, pathogen component, or cellularcomponent that directly or indirectly aids a pathogen. Such effectordomains include, for example and without limitation, an antibody,antibody fragment, single-chain antibody, peptidomimetic, or synthesizedmolecule. An effector domain can also be an antisense polynucleotide orsmall interfering RNA (G. M. Barton and R. Medzhitov (2002) Proc. Natl.Acad. Sci. USA 99, 14943-14945) that inhibits expression of a pathogengene or a host gene that aids a pathogen. An effector domain can also beDNA or RNA that encodes a molecule that binds to a pathogen, pathogencomponent, or cellular component that directly or indirectly aids apathogen. In addition, an effector domain can be any molecule thatsynthesizes a molecule that binds to a pathogen, pathogen component, orcellular component that directly or indirectly aids a pathogen.

Other effector domains can be isolated from complement pathway-relatedmolecules (W. E. Paul (ed.), Fundamental Immunology (4th ed.,Lippincott-Raven, Philadelphia, 1999), Chapter 29; M. K. Pangburn et al.(2000) Journal of Immunology 164, 4742-4751), for example and withoutlimitation, the following molecules or DNA or RNA encoding them: C3alpha, C3 beta, factor B, factor D, properdin, C1q, C1r, C1s, C4, C2,C5, C6, C7, C8, C9, factor I, factor H, C1-INH, C4 bp, S protein,clusterin, carboxypeptidase N, FHL-1, FHR-1, FHR-2, FHR-3, FHR-4, CR1,or DAF. An effector domain can also be isolated from a molecule thatbinds to, stimulates, or inhibits natural complement pathway-relatedmolecules such as those listed supra.

Other effector domains can be isolated from toll-like receptors, theiraccessory molecules, or molecules that they activate directly orindirectly, (S. Akira (2003) Current Opinion in Immunology 15, 5-11; T.Vasselon and P. A. Detmers (2002) Infection and Immunity 70, 1033-1041;C. A. Janeway Jr. and R. Medzhitov (2002) Annu. Rev. Immunol. 20,197-216), including for example and without limitation, the followingmolecules or DNA or RNA encoding them: toll-like receptor 1, Homosapiens (NCBI Accession #NP_(—)003254, AAC34137); toll-like receptor 2,Homo sapiens (NCBI Accession #AAH33756, AAM23001, AAC34133); toll-likereceptor 3, Homo sapiens (NCBI Accession #AAC34134, NP_(—)003256);toll-like receptor 4, Homo sapiens (NCBI Accession #AAC34135, AAF89753,AAF07823, AAF05316); toll-like receptor 5, Homo sapiens (NCBI Accession#AAC34136, BAB43955); toll-like receptor 6, Homo sapiens (NCBI Accession#NP_(—)006059, BAA78631); toll-like receptor 7, Homo sapiens (NCBIAccession #AAF60188, AAF78035, NP_(—)057646, AAH33651); toll-likereceptor 8, Homo sapiens (NCBI Accession #AAF64061, AAF78036); toll-likereceptor 9 Homo sapiens (NCBI Accession # AAG01734, AAG01735, AAG01736,BAB19259); toll-like receptor 10, Homo sapiens (NCBI Accession#AAK26744, NP_(—)112218); CD 14, Homo sapiens (NCBI Accession #AAH10507,AAL02401, CAD36116); MD-2, Homo sapiens (NCBI Accession #NP_(—)056179,BAA78717, AAH20690); MD-1, Homo sapiens (NCBI Accession #AAC98152,NP_(—)004262); RP105, Homo sapiens (NCBI Accession #BAA12019); toll/IL-1receptor domain containing adaptor protein (TIRAP), Homo sapiens (NCBIAccession #NP_(—)683708, NP_(—)443119, AAL05627); MyD88, Homo sapiens(NCBI Accession #AAB49967, AAC50954); IL-1R activated kinase 4 (IRAK-4),Homo sapiens (NCBI Accession #CAC60090); TNF-receptor-associated factor6 (TRAF6), Homo sapiens (NCBI Accession #NP_(—)665802, NP_(—)004611);toll-like receptor 1, Mus musculus (NCBI Accession #AAG35062, AAG37302,NP_(—)109607); toll-like receptor 2, Mus musculus (NCBI Accession#AAD46481, AAF04277, AAD49335, NP_(—)036035, AAF28345); toll-likereceptor 3, Mus musculus (NCBI Accession #AAK26117, AAL27007,NP_(—)569054); toll-like receptor 4, Mus musculus (NCBI Accession#AAD29272, AAF04278, AAF05317, NP_(—)067272, AAH29856); toll-likereceptor 5, Mus musculus (NCBI Accession #AAF65625, NP_(—)058624);toll-like receptor 6, Mus musculus (NCBI Accession #BAA78632, AAG38563,NP_(—)035734); toll-like receptor 7, Mus musculus (NCBI Accession#AAK62676, NP_(—)573474, AAL73191, AAL73192); toll-like receptor 8, Musmusculus (NCBI Accession #NP_(—)573475, AAK62677); toll-like receptor 9,Mus musculus (NCBI Accession #BAB19260, AAK29625, AAK28488,NP_(—)112455); CD14, Mus musculus (NCBI Accession #CAA32166, BAB68578,NP_(—)033971); MD-2, Mus musculus (NCBI Accession #BAA93619); MD-1, Musmusculus (NCBI Accession #BAA32399); RP105, Mus musculus (NCBI Accession#BAA07043); toll/IL-1 receptor domain containing adaptor protein(TIRAP), Mus musculus (NCBI Accession #AAL05628, NP_(—)473437); MyD88,Mus musculus (NCBI Accession #AAC53013); IL-IR activated kinase 4(IAK-4), Mus musculus (NCBI Accession #AAM15773, NP_(—)084202); orTNF-receptor-associated factor 6 (TRAF6), Mus musculus (NCBI Accession#BAA12705, NP_(—)033450). An effector domain can also be isolated from amolecule that binds to, stimulates, or inhibits naturaltoll-like-receptor response-related molecules such as those listedsupra.

Still other effector domains can be isolated from nucleotide-bindingoligomerization domain (NOD), or nucleotide-binding-domain (NBD), ornucleotide-binding-site (NBS), proteins or molecules that they activatedirectly or indirectly, (N. Inohara et al. (2002) Current Opinion inMicrobiology 5, 76-80; S. E. Girardin et al. (2002) TRENDS inMicrobiology 10, 193-199; J. A. Harton et al. (2002) Journal ofImmunology 169, 4088-4093; N. Inohara et al. (2000) Journal ofBiological Chemistry 275, 27823-27831), including for example andwithout limitation, the following molecules or DNA or RNA encodingthem:Nod1/CARD4 (Homo sapiens, #AAD28350, AAD43922; N. Inohara et al.(1999) Journal of Biological Chemistry 274, 14560-14567); Nod2, (Homosapiens, #AAG33677, AAK70863, AAK70865, AAK70866, AAK70867, AAK70868; Y.Ogura et al. (2001) Journal of Biological Chemistry 276, 4812-4818; N.Inohara et al. (2003) Journal of Biological Chemistry, PMID: 12514169);Ipaf-1/CLAN/CARD12 (Homo sapiens, #NM_(—)021209, AY035391; J.-L. Poyetet al. (2001) Journal of Biological Chemistry 276, 28309-28313); CIITA(Homo sapiens, #AY084054, AY084055, AF410154, NM_(—)000246, X74301; M.W. Linhoff et al. (2001) Molecular and Cellular Biology 21, 3001-3011;A. Muhlethaler-Mottet et al. (1997) EMBO Journal 16, 2851-2860); NAIP(Homo sapiens, #U21912, U19251); Defcap/NAC/NALP1/CARD7 (Homo sapiens,#NM_(—)033004, NM_(—)033005, NM_(—)033006, NM_(—)033007, NM_(—)014922);NBS1/NALP2 (Homo sapiens, #AF310106, NM_(—)017852); cryopyrin/CIAS1(Homo sapiens, #AF410477, AF427617, AH011140, NM_(—)004895); RIP (Homosapiens, #U50062; S. Grimm et al. (1996) Proc. Natl. Acad. Sci. USA 93,10923-10927; H. Hsu et al. (1996) Immunity 4, 387-396);Rip2/RICK/CARDIAK (Homo sapiens, #AF064824, AF078530; N. Inohara et al.(1998) Journal of Biological Chemistry 273, 18675; M. Thome et al.(1998) Current Biology 8, 885-888); and PKK (A. Muto et al. (2002)Journal of Biological Chemistry 277, 31871-31876). An effector domaincan also be isolated from a molecule that binds to, stimulates, orinhibits natural NOD-response-related molecules such as those listedsupra.

Effector domains can also be isolated from pentraxins or molecules thatthey activate directly or indirectly, (H. Gewurz et al. (1995) CurrentOpinion in Immunology 7, 54-64), including for example and withoutlimitation, the following molecules or DNA or RNA encoding them:C-reactive protein (CRP), Homo sapiens (NCBI Accession #1GNHA, 1GNHB,1GNHC, 1GNHD, 1GNHE, 1GNHF, 1GNHG, 1GNHH, 1GNHI, 1GNHJ); C-reactiveprotein (CRP), Mus musculus (NCBI Accession #CAA31928, NP_(—)031794);serum amyloid P component (SAP), Homo sapiens (NCBI Accession #1SACA,1SACB, 1SACC, 1SACD, 1SACE); and serum amyloid P component (SAP), Musmusculus (NCBI Accession #NP_(—)035448, CAA34774). An effector domaincan also be isolated from a molecule that binds to, stimulates, orinhibits natural pentraxin-response-related molecules such as thoselisted supra.

Other effector domains can be isolated from collectins or molecules thatthey activate directly or indirectly, (M. Gadjeva et al. (2001) CurrentOpinion in Immunology 13, 74-78; U. L. Holmskov (2000) APMIS Suppl. 100,1-59), including for example and without limitation, the followingmolecules or DNA or RNA encoding them: mannan/mannose binding lectin(MBL), Homo sapiens (NCBI Accession #AAK52907, CAB56120, CAB56044);mannan/mannose binding lectin (MBL), Mus musculus (NCBI Accession#NP_(—)034905, NP_(—)034906); MBL-associated serine protease 1 (MASP1),Homo sapiens (NCBI Accession #NP_(—)001870, NP_(—)624302);MBL-associated serine protease 2 (MASP2), Homo sapiens (NCBI Accession#NP_(—)006601, NP_(—)631947, AAG50274, BAA85659); MBL-associated serineprotease 1 (MASP1), Mus musculus (NCBI Accession #XP_(—)193834);MBL-associated serine protease 2 (MASP2), Mus musculus (NCBI Accession#BAA34674, CAB65247, CAB65250); MBL-associated serine protease 3(MASP3), Mus musculus (NCBI Accession #BAB69688); surfactant protein A(SP-A), Homo sapiens (NCBI Accession #NP_(—)005402, NP_(—)008857);surfactant protein D (SP-D), Homo sapiens (NCBI Accession #CAA46152,NP_(—)003010); surfactant protein D (SP-D), Mus musculus (NCBI Accession#AAF15277); surfactant protein D (SP-D), Bos taurus (NCBI Accession#CAA53510, S33603); conglutinin, Bos taurus (NCBI Accession #CAA50665,BAA03170); collectin-43 (CL-43), Bos taurus (NCBI Accession #CAA53511,P42916, A53570); collectin-L1, Mus musculus (NCBI Accession #BAC53954);or collectin placenta 1 (CL-P1), Homo sapiens (NCBI Accession#AB005145). An effector domain can also be isolated from a molecule thatbinds to, stimulates, or inhibits natural collectin response-relatedmolecules such as those listed supra.

Still other effector domains can be isolated from mannose receptors ormolecules that they activate directly or indirectly, (L. East and C. M.Isacke (2002) Biochimica et Biophysica Acta 1572, 364-386; S. Zamze etal. (2002) Journal of Biological Chemistry 277, 41613-41623), includingfor example and without limitation, the following molecules or DNA orRNA encoding them: mannose receptor (MR), Homo sapiens (NCBI Accession#NM_(—)002438); and mannose receptor (MR), Mus musculus (NCBI Accession#CAA78028, NP_(—)032651, NP_(—)032652). An effector domain can also beisolated from a molecule that binds to, stimulates, or inhibits naturalmannose-receptor-response-related molecules such as those listed supra.

Effector domains can also be isolated from scavenger receptors ormolecules that they activate directly or indirectly, (L. Peiser et al.(2002) Current Opinion in Immunology 14, 123-128; A. Brannstrom et al.(2002) Biochemical and Biophysical Research Communications 290,1462-1469), including for example and without limitation, the followingmolecules or DNA or RNA encoding them: scavenger receptor A I (SR-A I),Homo sapiens (NCBI Accession #D90187); scavenger receptor A II (SR-AII), Homo sapiens (NCBI Accession #D90188); scavenger receptor A I (SR-AI), Mus musculus (NCBI Accession #L04274); scavenger receptor A II (SR-AII), Mus musculus (NCBI Accession #L04275); macrophage receptor withcollagenous structure (MARCO), Homo sapiens (NCBI Accession#NP_(—)006761); macrophage receptor with collagenous structure (MARCO),Mus musculus (NCBI Accession #NP_(—)034896); scavenger receptor withC-type lectin I (SR-CL I), Homo sapiens (NCBI Accession #BAB39147);scavenger receptor with C-type lectin II (SR-CL II), Homo sapiens(NCBIAccession #BAB39148); and scavenger receptor with C-type lectin (SR-CL),Mus musculus (NCBI Accession #BAB82497). An effector domain can also beisolated from a molecule that binds to, stimulates, or inhibits naturalscavenger receptor response-related molecules such as those listedsupra.

An effector domain can be isolated from a molecule that inhibitstransport between the cytoplasm and the nucleus of a cell, including forexample and without limitation, the following molecules or DNA or RNAencoding them: importin alpha 1 (Homo sapiens, #NM_(—)002266) with theimportin beta binding domain (approximately amino acids 3-99) removed;importin alpha 3 (Homo sapiens, #NM_(—)002268) with the importin betabinding domain (approximately amino acids 3-94) removed; importin alpha4 (Homo sapiens, #NM_(—)002267) with the importin beta binding domain(approximately amino acids 3-94) removed; importin alpha 5 (Homosapiens, #U28386) with the importin beta binding domain (approximatelyamino acids 3-94) removed; importin alpha 6 (Homo sapiens,#NM_(—)002269) with the importin beta binding domain (approximatelyamino acids 3-94) removed; importin alpha 7 (Homo sapiens,#NM_(—)012316) with the importin beta binding domain (approximatelyamino acids 3-103) removed; importin alpha with the importin betabinding domain removed as described supra and also with the last twoarmadillo repeats removed (Y. Miyamoto et al. (2002) EMBO Journal 21,5833-5842), as will be understood by one of skill in the art; theautoinhibitory domain of an importin alpha mutated to have a higher thannormal affinity for wild-type importin alpha (B. Catimel et al. (2001)Journal of Biological Chemistry 276, 34189-34198), as will be understoodby one of skill in the art; a modified importin alpha that does notenable nuclear import, but still binds to one or more pathogen nuclearlocalization signals (NLSs), preferably with a higher affinity than itbinds to cellular NLSs, as will be understood by one of skill in theart; the importin beta binding domain of importin alpha 1 (Homo sapiens,#NM_(—)002266, approximately amino acids 1-99); the importin betabinding domain of importin alpha 3 (Homo sapiens, #NM_(—)002268,approximately amino acids 1-94); the importin beta binding domain ofimportin alpha 4 (Homo sapiens, #NM_(—)002267, approximately amino acids1-94); the importin beta binding domain of importin alpha 5 (Homosapiens, #U28386, approximately amino acids 1-94); the importin betabinding domain of importin alpha 6 (Homo sapiens, #NM_(—)002269,approximately amino acids 1-94); the importin beta binding domain ofimportin alpha 7 (Homo sapiens, #NM_(—)012316, approximately amino acids1-103); importin beta 1 (Homo sapiens, #NM_(—)002265, #NP_(—)002256)modified to not bind nucleoporins, for example by deleting the regionbetween HEAT-5 and HEAT-6 (approximately amino acids 203-211) and theregion between HEAT-6 and HEAT-7 (approximately amino acids 246-252) orby replacing those regions with nonhomologous linker regions (Y. M.Chook and G. Blobel (2001) Current Opinion in Structural Biology 11,703-715); importin beta 1 (Homo sapiens, #NM_(—)002265, #NP_(—)002256)modified to not bind importin alpha, for example by deleting the acidicloop importin-alpha-binding region spanning from approximately aminoacid 333 through approximately amino acid 343 (G. Cingolani et al.(1999) Nature 399, 221-229); a defective mutant of an exportin (I. G.Macara (2001) Microbiology and Molecular Biology Reviews 65, 570-594) aswill be understood by one of skill in the art; a mutant p10/NTF2 thatinhibits import by importin beta 1, for example, p10 D23A (C. M. Lane etal. (2000) Journal of Cell Biology 151, 321-331) or N77Y (B. B. Quimbyet al. (2001) Journal of Biological Chemistry 276, 38820-38829);vesicuovirus matrix protein or a portion thereof that inhibits nuclearimport and/or nuclear export (J. M. Petersen et al. (2001) Proc. Natl.Acad. Sci. USA 98, 8590-8595; J. M. Petersen et al. (2000) Molecular andCellular Biology 20, 8590-8601; C. von Kobbe et al. (2000) MolecularCell 6, 1243-1252); a peptide or other molecule that resembles theclassical nuclear localization signal of SV40 T antigen (E. Merle et al.(1999) Journal of Cellular Biochemistry 74, 628-637); peptides with FxFGrepeats or GLFG repeats (R. Bayliss et al. (2002) Journal of BiologicalChemistry 277, 50597-50606); leptomycin B; or a mutant of Ran thatinterferes with nuclear import or export, for example and withoutlimitation, RanC4A (R. H. Kehlenbach et al. (2001) Journal of BiologicalChemistry 276, 14524-14531).

An effector domain can be isolated from any naturally or non-naturallyoccurring molecule that binds to a pathogen, pathogen component, orcellular component that is involved in transport between the cytoplasmand the nucleus of a cell (I. G. Macara (2001) Microbiology andMolecular Biology Reviews 65, 570-594; B. Ossareh-Nazari (2001) Traffic2, 684-689). Such effector molecules include, for example and withoutlimitation, an antibody, antibody fragment, single-chain antibody,peptidomimetic, or synthesized molecule. An effector molecule can alsobe DNA or RNA that encodes a molecule that binds to a pathogen, pathogencomponent, or cellular component that is involved in transport betweenthe cytoplasm and the nucleus of a cell. In addition, an effectormolecule can be any molecule that synthesizes a molecule that binds to apathogen, pathogen component, or cellular component that is involved intransport between the cytoplasm and the nucleus of a cell.

Cellular components that are involved in transport between the cytoplasmand the nucleus of a cell (I. G. Macara (2001) Microbiology andMolecular Biology Reviews 65, 570-594; E. Conti and E. Izaurralde (2001)Current Opinion in Cell Biology 13, 310-319) include, for example,importin alpha proteins, importin beta proteins, importin 7, Ran, Nup358(S. K. Vasu and D. J. Forbes (2001) Current Opinion in Cell Biology 13,363-375), CAN/Nup214 (L. C. Trotman et al. (2001) Nature Cell Biology 3,1092-1100; S. K. Vasu and D. J. Forbes (2001) Current Opinion in CellBiology 13, 363-375), CRM1, CAS, calreticulin, or kinases orphosphatases that regulate nuclear import or export (R. H. Kehlenbachand L. Gerace (2000) Journal of Biological Chemistry 275, 17848-17856).In one embodiment, the effector domain inhibits pathogen transport moreefficiently than cellular transport.

An effector domain can be isolated from a molecule that alters theendocytic or phagocytic pathways (for example and without restriction,the properties of endosomes, phagosomes, lysosomes, other intracellularcompartments, or vesicular trafficking) to produce an anti-pathogeneffect, (L. A. Knodler, J. Celli, and B. B. Finlay (2001) Nat. Rev. Mol.Cell. Biol. 2, 578-588; D. Sacks and A. Sher (2002) Nature Immunology 3,1041-1047; M. W. Hornef et al. (2002) Nature Immunology 3, 1033-1040; J.Pieters (2001) Current-Opinion in Immunology 13, 37-44), for example andwithout limitation, the following molecules or DNA or RNA encoding them:dynamin-1 mutant K44A (M. Huber et al. (2001) Traffic 2, 727-736),particularly when overexpressed; cellubrevin (R. A. Fratti et al. (2002)Journal of Biological Chemistry 277, 17320-17326), particularly whenoverexpressed; Salmonella SpiC protein (NCBI Accession #U51927); adefective mutant of TassC (A. H. Lee et al. (2002) Cell. Microbiol. 4,739-750); other vesicular trafficking inhibitors; Nramp1 (P.Cuellar-Mata et al. (2002) Journal of Biological Chemistry 277,2258-2265; C. Frehel et al. (2002) Cellular Microbiology 4, 541-556; D.J. Hackam et al. (1998) J. Exp. Med. 188, 351-364), particularly whenoverexpressed; NADPH oxidase subunits or cofactors (P. V. Vignais (2002)Cell. Mol. Life Sci. 59, 1428-1459), particularly when overexpressed;NOS2 nitric oxide synthase (J. D. MacMicking et al. (1997) Proc. Natl.Acad. Sci. USA 94, 5243-5248), particularly when overexpressed; humanpapillomavirus 16 E5 protein (NCBI Accession #W5WLHS); bafilomycin A1;an antibody, single-chain antibody, or other molecule that binds toV-ATPase subunit a (S. B. Sato and S. Toyama (1994) J. Cell. Biol. 127,39-53), preferably a1 or a2; antisense oligonucleotides that inhibitvacuolar ATPase subunits (J. E. Strasser et al. (1999) Journal ofImmunology 162, 6148-6154); a peptide composed of approximately the 78amino-terminal amino acids of vacuolar H+-ATPase subunit E (M. Lu et al.(2002) Journal of Biological Chemistry 277, 38409-38415); A2-cassettemutant of vacuolar H+-ATPase subunit A (N. Hernando et al. (1999) Eur.J. Biochem. 266, 293-301); a defective mutant of subunit a1 or a2 ofvacuolar H+-ATPase (S. Kawasaki-Nishi et al. (2001) Proc. Natl. Acad.Sci. USA 98, 12397-12402; S. Kawasaki-Nishi et al. (2001) 276,47411-47420; T. Nishi and M. Forgac (2000) J. Biol. Chem. 275,6824-6830; S. B. Peng et al. (1999) J. Biol. Chem. 274, 2549-2555; T.Toyomura et al. (2000) J. Biol. Chem. 275, 8760-8765); overexpression ofthe C and/or H subunits of vacuolar H+-ATPase subunit E (K. K. Curtisand P. M. Kane (2002) Journal of Biological Chemistry 277, 2716-2724);other defective vacuolar ATPase subunit or portion of a subunit(examples of wild-type human vacuolar ATPase subunits that can be madedefective for anti-pathogen effects will be understood by one of skillin the art, and include, without limitation, those vacuolar ATPasesubunits with Accession numbers: NM_(—)004231, NM_(—)130463,NM_(—)015994, NM_(—)001694, NM_(—)004047, NM_(—)001696, NM_(—)004691,NM_(—)001695, NM_(—)001693, NM_(—)001690, NM_(—)020632, NM_(—)004888);other vacuolar H+-ATPase inhibitors, particularly inhibitors that alterpH in endosomes, phagosomes, or lysosomes with minimal undesirableeffects on cells such as osteoclasts and renal intercalated cells;molecules that inhibit intracellular compartment acidification and canbe isolated from intracellular pathogens (for example and withoutlimitation, Mycobacterium spp., Salmonella spp., Yersinia spp.,Chlamydia spp., Histoplasma capsulatum (J. E. Strasser et al. (1999)Journal of Immunology 162, 6148-6154), or Toxoplasma gondii); moleculesthat promote intracellular compartment acidification and can be isolatedfrom intracellular pathogens (for example and without limitation,Coxiella burnetti, Francisella tularensis, Brucella spp. (F. Porte etal. (1999) Infection and Immunity 67, 4041-4047), Leishmania spp.,Listeria monocytogenes, Bordetella bronchiseptica, or Legionellapneumophila); or molecules that interfere with vesicular trafficking orother properties of intracellular compartments can be isolated fromintracellular pathogens (for example and without limitation,Mycobacterium spp., Salmonella spp., Yersinia spp., Chlamydia spp.,Histoplasma capsulatum (J. E. Strasser et al. (1999) Journal ofImmunology 162, 6148-6154), Toxoplasma gondii, Coxiella burnetti,Francisella tularensis, Brucella spp. (F. Porte et al. (1999) Infectionand Immunity 67, 4041-4047), Leishmania spp., Listeria monocytogenes,Bordetella bronchiseptica, or Legionella pneumophila)

An effector domain can be isolated from a molecule that stimulates,inhibits, or binds to a component of the ubiquitin-proteasomedegradative pathway (M. H. Glickman and A. Ciechanover (2002) Physiol.Rev. 82, 373-428; K. M. Sakamoto (2002) Molecular Genetics andMetabolism 77, 44-56) to produce an anti-pathogen effect, for exampleand without limitation, the following molecules or DNA or RNA encodingthem: CHIP (D. M. Cyr et al. (2002) Trends Biochem. Sci. 27, 368-375; J.Demand et al. (2001) Curr. Biol. 11, 1569-1577; S. Murata et al. (2001)EMBO Rep. 2, 1133-1138), particularly when overexpressed; Fbx2 (Y.Yoshida et al. (2002) Nature 418, 438-442), particularly whenoverexpressed; molecules that ubiquitinate pathogens, pathogencomponents, or cellular components that assist pathogens (P. Zhou et al.(2000) Mol. Cell 6, 751-756; K. M. Sakamoto et al. (2001) Proc. Natl.Acad. Sci. USA 98, 8554-8559; N. Zheng et al. (2000) Cell 102, 533-539;D. Oyake et al. (2002) Biochemical and Biophysical ResearchCommunications 295, 370-375); or inhibitors of ubiquitination orproteasomes (J. Myung et al. (2001) Medicinal Research Reviews 21,245-273; G. Lennox et al. (1988) Neurosci. Lett. 94, 211-217; N. F.Bence et al. (2001) Science 292, 1552-1555), for example and withoutlimitation, lactacystin or epoxomicin.

Effector domains can be isolated from molecules that execute, stimulate,or inhibit defensin-related responses (R. I. Lehrer and T. Ganz (2002)Current Opinion in Immunology 14, 96-102; D. Yang et al. (2002) TRENDSin Immunology 23, 291-296; P. A. Raj and A. R. Dentino (2002) FEMSMicrobiology Letters 206, 9-18; G. T.-J. Huang et al. (2002) Human GeneTherapy 13, 2017-2025; J. Cohn et al. (2001) Current Opinion inImmunology 13, 55-62), for example and without limitation, the followingmolecules or DNA or RNA encoding them: alpha defensins, beta defensins,theta defensins, plant defensins, or arthropod defensins. An effectordomain can be isolated from a molecule that binds to, stimulates, orinhibits natural defensin-response related molecules such as thoselisted supra.

Other effector domains can be isolated from molecules that execute,stimulate, or inhibit cathelicidin-related responses (R. I. Lehrer andT. Ganz (2002) Curr. Opin. Hematol. 9, 18-22; B. Ramanathan et al.(2002) Microbes Infect. 4, 361-372; M. Zaiou and R. L. Gallo (2002) J.Mol. Med. 80, 549-561), for example and without limitation, thefollowing molecules or DNA or RNA encoding them: hCAP-18/LL-37, CRAMP,Bac4, OaBac5; prophenin-1, protegrin-1, or PR-39. An effector domain canbe isolated from a molecule that binds to, stimulates, or inhibitsnatural cathelicidin-response related molecules such as those listedsupra.

Still other effector domains can be isolated from molecules thatexecute, stimulate, or inhibit chemokine-related or thrombocidin-relatedresponses (M. Durr and A. Peschel (2002) Infection and Immunity 70,6515-6517; Y. Tang et al. (2002) Infection and Immunity 70, 6524-6533;J. Krijgsveld et al. (2000) Journal of Biological Chemistry 275,20374-20381; A. D. Luster (2002) Current Opinion in Immunology 14,129-135; M. Mellado et al. (2001) Annu. Rev. Immunol. 19, 397-421), forexample and without limitation, the following molecules or DNA or RNAencoding them: CC chemokines, CXC chemokines, C chemokines, CX3Cchemokines, CC chemokine receptors, CXC chemokine receptors, C chemokinereceptors, CX3C chemokine receptors, JAK proteins, STAT proteins,fibrinopeptide A, fibrinopeptide B, or thymosin beta 4. An effectordomains can be isolated from a molecule that binds to, stimulates, orinhibits natural chemokine-response-related orthrombocidin-response-related molecules such as those listed supra.

An effector domain can be isolated from a molecule that is toxic to aninfected host cell or a pathogen cell. In one embodiment, the effectormolecule is toxic to an infected host cell is not toxic to uninfectedhost cells, for example and without limitation, an intracellularbacterial toxin (B. B. Finlay and P. Cossart (1997) Science 276,718-725; C. Montecucco et al. (1994) FEBS Lett. 346, 92-98; P. O. Falneset al. (2001) Biochemistry 40, 4349-4358) that has been modified so thatit cannot cross cellular plasma membranes, such as the A (21 kDa)fragment of diptheria toxin. An effector domains can be isolated from amolecule that is toxic to a pathogen cell, including but not limited topenicillin, erythromycin, tetracycline, rifampin, amphotericin B,metronidazole, or mefloquine. An effector domains can be isolated froman ATP inhibitor (E. K. Hui and D. P. Nayak (2001) Virology 290,329-341). An effector molecule can be a toxin that inhibitstranscription, translation, replication, oxidative phosphorylation,cytoskeletal processes, or other cell and/or pathogen functions.

An effector domain can be isolated from a molecule that inhibits buddingor release of pathogens from an infected cell, for example and withoutlimitation, the following molecules or DNA or RNA encoding them: Hrs,particularly when overexpressed (N. Bishop et al. (2002) Journal of CellBiology 157, 91-101; L. Chin et al. (2001) Journal of BiologicalChemistry 276, 7069-7078; C. Raiborg et al. (2002) Nature Cell Biology4, 394-398); defective Vps4 mutants such as K173Q or E228Q, particularlywhen overexpressed (J. E. Garrus et al. (2001) Cell 107, 55-65); smallinterfering RNA that inhibits Tsg101 expression (N. Bishop et al. (2002)Journal of Cell Biology 157, 91-101; J. E. Garrus et al. (2001) Cell107, 55-65); truncated AP-50 consisting of approximately amino acids121-435, or other defective mutant of AP-50, particularly whenoverexpressed (B. A. Puffer et al. (1998) Journal of Virology 72,10218-10221); WW-domain-containing fragment of LDI-1, Nedd4,Yes-associated protein, KIAA0439 gene product, or other defectiveNedd4-related proteins, particularly when overexpressed (A. Kikonyogo etal. (2001) Proc. Natl. Acad. Sci. USA 98, 11199-11204; A. Patnaik and J.W. Wills (2002) Journal of Virology 76, 2789-2795); a peptide consistingof the HIV p6 Gag PTAPP-motif-containing late (L) domain (L. VerPlank etal. (2001) Proc. Natl. Acad. Sci. USA 98, 7724-7729) or other viral late(L) domain containing PTAP, PSAP, PPXY, YPDL, or YXXL motifs (J.Martin-Serrano et al. (2001) Nature Medicine 7, 1313-1319; A. Patnaikand J. W. Wills (2002) Journal of Virology 76, 2789-2795); amino acids1-167 of Tsg101, TSG-5′ fragment of Tsg101, or similar amino-terminalfragment of Tsg101, particularly when overexpressed (D. G. Demirov etal. (2002) Proc. Natl. Acad. Sci. USA 99, 955-9601; E. L. Myers and J.F. Allen (2002) Journal of Virology 76, 11226-11235); a mutant of Tsg101(M. Babst et al. (2000) Traffic 1, 248-258; L. VerPlank et al. (2001)Proc. Natl. Acad. Sci. USA 98, 7724-7729; J. Martin-Serrano et al.(2001) Nature Medicine 7, 1313-1319; O. Pornillos et al. (2002) EMBOJournal 21, 2397-2406) with reduced capacity to aid viral budding; acasein kinase 2 (CK2) inhibitor, such as the peptide RRADDSDDDDD (SEQ IDNO: 472)(E. K. Hui and D. P. Nayak (2002) Journal of General Virology83, 3055-3066); or G protein signalling inhibitors (E. K. Hui and D. P.Nayak (2002) Journal of General Virology 83, 3055-3066). An effectordomain can be isolated from a molecule that binds to a cellular orpathogen molecule (for example and without limitation, to one or more ofthe following molecules: Tsg101, Vps4, casein kinase 2, Hrs, hVps28,Eap30, Eap20, Eap45, Chmp1, Chmp2, Chmp3, Chmp4, Chmp5, Chmp6, AP-50,Nedd4-related proteins, WW-domain-containing proteins, orL-domain-containing proteins; O. Pornillos et al. (2002) TRENDS in CellBiology 12, 569-579; P. Gomez-Puertas et al. (2000) Journal of Virology74, 11538-11547; E. Katz et al. (2002) Journal of Virology 76,11637-11644) that is involved in budding or release of pathogens from aninfected cell.

An effector domain can be isolated from a molecule that degradescomponents of cells or pathogens, for example and without limitation:proteases, including chymotrypsin, trypsin, or elastase; DNases,including caspase-activated DNase (CAD), constitutively active CAD (N.Inohara et al. (1999) Journal of Biological Chemistry 274, 270-274), orrestriction enzymes; RNases, including RNase II (Homo sapiens,#AF189011; Escherichia coli, #NP_(—)417062, NC_(—)000913), RNt1p(Saccharomyces cerevisiae, #U27016), Pac1, (Schizosaccharomyces pombe,#X54998), RNase A, or RNase L; glycosidases, including N-glycanase,endoglycosidase H, O-glycanase, endoglycosidase F2, sialidase, orbeta-galactosidase; or lipases, including to phospholipase A1,phospholipase A2, phospholipase C, or phospholipase D. An effectordomain can be encoded by DNA or RNA which encodes a molecule thatdegrades components of cells or pathogens. An effector domain can beisolated from a molecule that binds to, stimulates, or inhibits amolecule such as those described supra that degrades components of cellsor pathogens.

Other effector domain can be isolated from molecules that execute,stimulate, or inhibit immune-related responses (W. E. Paul (ed.),Fundamental Immunology (4th ed., Lippincott-Raven, Philadelphia, 1999)),for example and without limitation, the following molecules or DNA orRNA encoding them: MHC Class I, MHC Class II, antibodies, single-chainantibodies, T cell receptors, Fc receptors, NK cell activation receptors(including but not limited to NKp46, Ly49H, and NKG2D; A. Diefenbach andD. H. Raulet (2003) Current Opinion in Immunology 15, 37-44; A. R.French and W. M. Yokoyama (2003) Current Opinion in Immunology 15,45-51), NK cell inhibitory receptors, receptor-associated tyrosinekinases, or phospholipase C. An effector domain can be isolated from amolecule that binds to, stimulates, or inhibits natural immune-responserelated molecules.

A chimeric molecule of the invention that has at least one dsRNA bindingdomain as described supra, can be bound to, or is associated with, aneffector domain that mediates the activation or induction of apoptosis.For example, caspases (also known as pro-caspases) 1 to 14 (Caspase 1,Homo sapiens, #NM_(—)001223; Caspase 2, Homo sapiens, #NM_(—)032982,NM_(—)001224, NM_(—)032983, and NM_(—)032984; Caspase 3, Homo sapiens,#U26943; Caspase 4, Homo sapiens, #AAH17839; Caspase 5, Homo sapiens,#NP_(—)004338; Caspase 6, Homo sapiens, #NM_(—)001226 and NM_(—)032992;Caspase 7, Homo sapiens, #XM_(—)053352; Caspase 8, Homo sapiens,#NM_(—)001228; Caspase 9, Homo sapiens, #AB019197; Caspase 10, Homosapiens, #XP_(—)027991; Caspase 13, Homo sapiens, #AAC28380; Caspase 14,Homo sapiens, #NP_(—)036246; Caspase 1, Mus musculus, #BC008152; Caspase2, Mus musculus, #NM_(—)007610; Caspase 3, Mus musculus, #NM_(—)009810;Caspase 6, Mus musculus, #BC002022; Caspase 7, Mus musculus, #BC005428;Caspase 8, Mus musculus, #BC006737; Caspase 9, Mus musculus,#NM_(—)015733; Caspase 11, Mus musculus, #NM_(—)007609; Caspase 12, Musmusculus, #NM_(—)009808; Caspase 14, Mus musculus, #AF092997; CED-3caspase, and Caenorhabditis elegans, #AF210702) can be effector domains.Such caspases are widely recognized in the art and include homologs froma variety of organisms, including Homo sapiens, Mus musculus, Drosophilamelanogaster and C. elegans. Both a full-length pro-caspase and afragment of a pro-caspase that contains the active caspase subunits andthe activation cleavage sites are suitable for use in the invention, aswill be appreciated by one of skill in the art.

Other effector domains that mediate the activation or induction ofapoptosis include apoptosis-associated proteins, such as a deatheffector domain (DED) isolated from FADD, a caspase recruitment domain(CARD) isolated from Apaf-1, or a death domain (DD) isolated from eitherFas or TRADD (tumor necrosis factor receptor type 1 (TNFR1)-associateddeath domain protein). Table 2 provides examples of these effectordomain-containing proteins and the approximate amino acid position ofthe effector domains. TABLE 2 NCBI Accession Protein, organism Domaintype: sequence location (amino acids) number FADD, Homo sapiens Deatheffector domain (DED): 1-100 U24231 FADD, Mus musculus Death effectordomain (DED): 18-69 NM_010175 Apaf-1, Homo sapiens Caspase recruitmentdomain (CARD): NM_013229, 1-89 NM_001160 Apaf-1, Mus musculus Caspaserecruitment domain (CARD): NP_033814 1-87 TRADD, Homo sapiens Deathdomain (DD): 226-301 NP_003780, CAC38018

In a preferred embodiment, the chimeric molecule or agent of theinvention has one or more dsRNA-binding domains, as described supra,fused in frame with or bound to or associated with one or more of thefollowing effector molecules: an apoptosis effector domain as describedsupra; an effector domain from RNase L (for example, approximately aminoacids 336-741 of human RNase L); an effector domain from PERK (forexample, approximately amino acids 543-1115 of human PERK); an effectordomain from IRE1 alpha (for example, approximately amino acids 470-977of human IRE1 alpha); an effector domain from IRE1 beta (for example,approximately amino acids 452-925 of human IRE1 beta); an effectordomain from Nod1/CARD4 (for example, approximately amino acids 1-126 ofhuman Nod1/CARD4); an effector domain from Nod2 (for example,approximately amino acids 1-250 of human Nod2); an effector domain fromIpaf-1/CLAN/CARD12 (for example, approximately amino acids 1-125 ofhuman Ipaf-1/CLAN/CARD12); an acidic domain effector domain from CIITA(for example, approximately amino acids 1-340 of CARD-less human CIITA);a CARD effector domain from dendritic cell CIITA (for example,approximately amino acids 1-100 of human dendritic cell CIITA); aCARD-acidic-domain effector domain from dendritic cell CIITA (forexample, approximately amino acids 1-440 of human dendritic cell CIITA);an effector domain from IKK gamma (for example, full-length human IKKgamma or approximately amino acids 1-200 of human IKK gamma); aneffector domain from HSF1 (for example, approximately amino acids 1-227of human HSF1); an effector domain from RIP (for example, approximatelyamino acids 1-300 of human RIP); or an effector domain fromRip2/RICK/CARDIAK (for example, approximately amino acids 1-300 of humanRip2/RICK/CARDIAK).

In another preferred embodiment, the chimeric molecule or agent of theinvention has one or more 2′,5′-oligoadenylate-binding domains, asdescribed supra, fused in frame with or bound to or associated with oneor more of the following effector molecules: an apoptosis effectordomain as described supra; an effector domain from protein kinase R (forexample, approximately amino acids 175-551 or 274-551 of human proteinkinase R); an effector domain from PERK (for example, approximatelyamino acids 543-1115 of human PERK); an effector domain from IRE1 alpha(for example, approximately amino acids 470-977 of human IRE1 alpha); aneffector domain from IRE1 beta (for example, approximately amino acids452-925 of human IRE1 beta); an effector domain from Nod1/CARD4 (forexample, approximately amino acids 1-126 of human Nod1/CARD4); aneffector domain from Nod2 (for example, approximately amino acids 1-250of human Nod2); an effector domain from Ipaf-1/CLAN/CARD12 (for example,approximately amino acids 1-125 of human Ipaf-1/CLAN/CARD12); an acidicdomain effector domain from CIITA (for example, approximately aminoacids 1-340 of CARD-less human CIITA); a CARD effector domain fromdendritic cell CIITA (for example, approximately amino acids 1-100 ofhuman dendritic cell CIITA); a CARD-acidic-domain effector domain fromdendritic cell CIITA (for example, approximately amino acids 1-440 ofhuman dendritic cell CIITA); an effector domain from IKK gamma (forexample, full-length human IKK gamma or approximately amino acids 1-200of human IKK gamma); an effector domain from HSF1 (for example,approximately amino acids 1-227 of human HSF1); an effector domain fromRIP (for, approximately amino acids 1-300 of human RIP); or an effectordomain from Rip2/RICK/CARDIAK (for example, approximately amino acids1-300 of human Rip2/RICK/CARDIAK).

In another preferred embodiment, the chimeric molecule or agent of theinvention has one or more endoplasmic-reticulum-stress-detection domainsfrom PERK (for example, approximately amino acids 1-542 of human PERK),fused in frame with or bound to or associated with one or more of thefollowing effector molecules: an apoptosis effector domain as describedsupra; an effector domain from protein kinase R (for example,approximately amino acids 175-551 or 274-551 of human protein kinase R);an effector domain from RNase L (for example, approximately amino acids336-741 of human RNase L); an effector domain from IRE1 alpha (forexample, approximately amino acids 470-977 of human IRE1 alpha); aneffector domain from IRE1 beta (for example, approximately amino acids452-925 of human IRE1 beta); an effector domain from Nod1/CARD4 (forexample, approximately amino acids 1-126 of human Nod1/CARD4); aneffector domain from Nod2 (for example, approximately amino acids 1-250of human Nod2); an effector domain from Ipaf-1/CLAN/CARD12 (for example,approximately amino acids 1-125 of human Ipaf-1/CLAN/CARD12); an acidicdomain effector domain from CIITA (for example, approximately aminoacids 1-340 of CARD-less human CIITA); a CARD effector domain fromdendritic cell CIITA (for example, approximately amino acids 1-100 ofhuman dendritic cell CIITA); a CARD-acidic-domain effector domain fromdendritic cell CIITA (for example, approximately amino acids 1-440 ofhuman dendritic cell CIITA); an effector domain from IKK gamma (forexample, full-length human IKK gamma or approximately amino acids 1-200of human IKK gamma); an effector domain from HSF1 (for example,approximately amino acids 1-227 of human HSF1); an effector domain fromRIP (for example, approximately amino acids 1-300 of human RIP); or aneffector domain from Rip2/RICK/CARDIAK (for example, approximately aminoacids 1-300 of human Rip2/RICK/CARDIAK).

In another preferred embodiment, the chimeric molecule or agent of theinvention has one or more endoplasmic-reticulum-stress-detection domainsfrom IRE1 alpha (for example, approximately amino acids 1-469 of humanIRE1 alpha), fused in frame with or bound to or associated with one ormore of the following effector molecules: an apoptosis effector domainas described supra; an effector domain from protein kinase R (forexample, approximately amino acids 175-551 or 274-551 of human proteinkinase R); an effector domain from RNase L (for example, approximatelyamino acids 336-741 of human RNase L); an effector domain from PERK (forexample, approximately amino acids 543-1115 of human PERK); an effectordomain from IRE1 beta (for example, approximately amino acids 452-925 ofhuman IRE1 beta); an effector domain from Nod1/CARD4 (for example,approximately amino acids 1-126 of human Nod1/CARD4); an effector domainfrom Nod2 (for example, approximately amino acids 1-250 of human Nod2);an effector domain from Ipaf-1/CLAN/CARD12 (for example, approximatelyamino acids 1-125 of human Ipaf-1/CLAN/CARD12); an acidic domaineffector domain from CIITA (for example, approximately amino acids 1-340of CARD-less human CIITA); a CARD effector domain from dendritic cellCIITA (for example, approximately amino acids 1-100 of human dendriticcell CIITA); a CARD-acidic-domain effector domain from dendritic cellCIITA (for example, approximately amino acids 1-440 of human dendriticcell CIITA); an effector domain from IKK gamma (for example, full-lengthhuman IKK gamma or approximately amino acids 1-200 of human IKK gamma);an effector domain from HSF1 (for example, approximately amino acids1-227 of human HSF1); an effector domain from RIP (for example,approximately amino acids 1-300 of human RIP); or an effector domainfrom Rip2/RICK/CARDIAK (for example, approximately amino acids 1-300 ofhuman Rip2/RICK/CARDIAK).

In another preferred embodiment, the chimeric molecule or agent of theinvention has one or more endoplasmic-reticulum-stress-detection domainsfrom IRE1 beta (for example, approximately amino acids 1-451 of humanIRE1 beta), fused in frame with or bound to or associated with one ormore of the following effector molecules: an apoptosis effector domainas described supra; an effector domain from protein kinase R (forexample, approximately amino acids 175-551 or 274-551 of human proteinkinase R); an effector domain from RNase L (for example, approximatelyamino acids 336-741 of human RNase L); an effector domain from PERK (forexample, approximately amino acids 543-1115 of human PERK); an effectordomain from IRE1 alpha (for example, approximately amino acids 470-977of human IRE1 alpha); an effector domain from Nod1/CARD4 (for example,approximately amino acids 1-126 of human Nod1/CARD4); an effector domainfrom Nod2 (for example, approximately amino acids 1-250 of human Nod2);an effector domain from Ipaf-1/CLAN/CARD12 (for example, approximatelyamino acids 1-125 of human Ipaf-1/CLAN/CARD12); an acidic domaineffector domain from CIITA (for example, approximately amino acids 1-340of CARD-less human CIITA); a CARD effector domain from dendritic cellCIITA (for example, approximately amino acids 1-100 of human dendriticcell CIITA); a CARD-acidic-domain effector domain from dendritic cellCIITA (for example, approximately amino acids 1-440 of human dendriticcell CIITA); an effector domain from IKK gamma (for example, full-lengthhuman IKK gamma or approximately amino acids 1-200 of human IKK gamma);an effector domain from HSF1 (for example, approximately amino acids1-227 of human HSF1); an effector domain from RIP (for example,approximately amino acids 1-300 of human RIP); or an effector domainfrom Rip2/RICK/CARDIAK (for example, approximately amino acids 1-300 ofhuman Rip2/RICK/CARDIAK).

In another preferred embodiment, the chimeric molecule or agent of theinvention has one or more stress-detection domains from HSF1 (forexample, approximately amino acids 125-503 of human HSF1), fused inframe with or bound to or associated with one or more of the followingeffector molecules: an apoptosis effector domain as described supra; aneffector domain from protein kinase R (for example, approximately aminoacids 175-551 or 274-551 of human protein kinase R); an effector domainfrom RNase L (for example, approximately amino acids 336-741 of humanRNase L); an effector domain from PERK (for example, approximately aminoacids 543-1115 of human PERK); an effector domain from IRE1 alpha (forexample, approximately amino acids 470-977 of human IRE1 alpha); aneffector domain from IRE1 beta (for example, approximately amino acids452-925 of human IRE1 beta); an effector domain from Nod 1/CARD4 (forexample, approximately amino acids 1-126 of human Nod1/CARD4); aneffector domain from Nod2 (for example, approximately amino acids 1-250of human Nod2); an effector domain from Ipaf-1/CLAN/CARD12 (for example,approximately amino acids 1-125 of human Ipaf-1/CLAN/CARD12); an acidicdomain effector domain from CIITA (for example, approximately aminoacids 1-340 of CARD-less human CIITA); a CARD effector domain fromdendritic cell CIITA (for example, approximately amino acids 1-100 ofhuman dendritic cell CIITA); a CARD-acidic-domain effector domain fromdendritic cell CIITA (for example, approximately amino acids 1-440 ofhuman dendritic cell CIITA); an effector domain from IKK gamma (forexample, full-length human IKK gamma or approximately amino acids 1-200of human IKK gamma); an effector domain from HSF1 (for example,approximately amino acids 1-227 of human HSF1); an effector domain fromRIP (for example, approximately amino acids 1-300 of human RIP); or aneffector domain from Rip2/RICK/CARDIAK (for example, approximately aminoacids 1-300 of human Rip2/RICK/CARDIAK).

In another preferred embodiment, the chimeric molecule or agent of theinvention has one or more LPS-binding domains, as described supra, fusedin frame with or bound to or associated with one or more of thefollowing effector molecules: an apoptosis effector domain as describedsupra; an effector domain from protein kinase R (for example,approximately amino acids 175-551 or 274-551 of human protein kinase R);an effector domain from RNase L (for example, approximately amino acids336-741 of human RNase L); an effector domain from PERK (for example,approximately amino acids 543-1115 of human PERK); an effector domainfrom IRE1 alpha (for example and without limitation, approximately aminoacids 470-977 of human IRE1 alpha); an effector domain from IRE1 beta(for example, approximately amino acids 452-925 of human IRE1 beta); aneffector domain from Nod1/CARD4 (for example, approximately amino acids1-126 of human Nod1/CARD4); an effector domain from Nod2 (for example,approximately amino acids 1-250 of human Nod2); an effector domain fromIpaf-1/CLAN/CARD12 (for example, approximately amino acids 1-125 ofhuman Ipaf-1/CLAN/CARD12); an acidic domain effector domain from CIITA(for example, approximately amino acids 1-340 of CARD-less human CIITA);a CARD effector domain from dendritic cell CIITA (for example,approximately amino acids 1-100 of human dendritic cell CIITA); aCARD-acidic-domain effector domain from dendritic cell CIITA (forexample, approximately amino acids 1-440 of human dendritic cell CIITA);an effector domain from IKK gamma (for example, full-length human IKKgamma or approximately amino acids 1-200 of human IKK gamma); aneffector domain from HSF1 (for example, approximately amino acids 1-227of human HSF1); an effector domain from RIP (for example, approximatelyamino acids 1-300 of human RIP); or an effector domain fromRip2/RICK/CARDIAK (for example, approximately amino acids 1-300 of humanRip2/RICK/CARDIAK).

In another preferred embodiment, the chimeric molecule or agent of theinvention has one or more apoptosis signal-detection domains from Apaf-1(for example, approximately amino acids 97-1194 of human Apaf-1), fusedin frame with or bound to or associated with one or more of thefollowing effector molecules: an apoptosis effector domain as describedsupra; an effector domain from protein kinase R (for example,approximately amino acids 175-551 or 274-551 of human protein kinase R);an effector domain from RNase L (for example, approximately amino acids336-741 of human RNase L); an effector domain from PERK (for example,approximately amino acids 543-1115 of human PERK); an effector domainfrom IRE1 alpha (for example, approximately amino acids 470-977 of humanIRE1 alpha); an effector domain from IRE1 beta (for example,approximately amino acids 452-925 of human IRE1 beta); an effectordomain from Nod1/CARD4 (for example, approximately amino acids 1-126 ofhuman Nod1/CARD4); an effector domain from Nod2 (for example,approximately amino acids 1-250 of human Nod2); an effector domain fromIpaf-1/CLAN/CARD12 (for example, approximately amino acids 1-125 ofhuman Ipaf-1/CLAN/CARD12); an acidic domain effector domain from CIITA(for example, approximately amino acids 1-340 of CARD-less human CIITA);a CARD effector domain from dendritic cell CIITA (for example,approximately amino acids 1-100 of human dendritic cell CIITA); aCARD-acidic-domain effector domain from dendritic cell CIITA (forexample, approximately amino acids 1-440 of human dendritic cell CIITA);an effector domain from IKK gamma (for example, full-length human IKKgamma or approximately amino acids 1-200 of human IKK gamma); aneffector domain from HSF1 (for example, approximately amino acids 1-227of human HSF1); an effector domain from RIP (for example, approximatelyamino acids 1-300 of human RIP); or an effector domain fromRip2/RICK/CARDIAK (for example, approximately amino acids 1-300 of humanRip2/RICK/CARDIAK).

In another preferred embodiment, the chimeric molecule or agent of theinvention has one or more apoptosis-signal-detection domains from FADD(for example, approximately amino acids 117-208 of human FADD), fused inframe with or bound to or associated with one or more of the followingeffector molecules: an apoptosis effector domain as described supra; aneffector domain from protein kinase R (for example, approximately aminoacids 175-551 or 274-551 of human protein kinase R); an effector domainfrom RNase L (for example, approximately amino acids 336-741 of humanRNase L); an effector domain from PERK (for example, approximately aminoacids 543-1115 of human PERK); an effector domain from IRE1 alpha (forexample, approximately amino acids 470-977 of human IRE1 alpha); aneffector domain from IRE1 beta (for example, approximately amino acids452-925 of human IRE1 beta); an effector domain from Nod1/CARD4 (forexample and without limitation, approximately amino acids 1-126 of humanNod1/CARD4); an effector domain from Nod2 (for example, approximatelyamino acids 1-250 of human Nod2); an effector domain fromIpaf-1/CLAN/CARD12 (for example, approximately amino acids 1-125 ofhuman Ipaf-1/CLAN/CARD12); an acidic domain effector domain from CIITA(for example, approximately amino acids 1-340 of CARD-less human CIITA);a CARD effector domain from dendritic cell CIITA (for example,approximately amino acids 1-100 of human dendritic cell CIITA); aCARD-acidic-domain effector domain from dendritic cell CIITA (forexample, approximately amino acids 1-440 of human dendritic cell CIITA);an effector domain from IKK gamma (for example, full-length human IKKgamma or approximately amino acids 1-200 of human IKK gamma); aneffector domain from HSF1 (for example, approximately amino acids 1-227of human HSF1); an effector domain from RIP (for example, approximatelyamino acids 1-300 of human RIP); or an effector domain fromRip2/RICK/CARDIAK (for example, approximately amino acids 1-300 of humanRip2/RICK/CARDIAK).

In another preferred embodiment, the chimeric molecule or agent of theinvention has one or more apoptosis-signal-detection domains fromcaspase 8 (for example, approximately amino acids 1-215 of human caspase8), fused in frame with or bound to or associated with one or more ofthe following effector molecules: an apoptosis effector domain asdescribed supra; an effector domain from protein kinase R (for example,approximately amino acids 175-551 or 274-551 of human protein kinase R);an effector domain from RNase L (for example, approximately amino acids336-741 of human RNase L); an effector domain from PERK (for example,approximately amino acids 543-1115 of human PERK); an effector domainfrom IRE1 alpha (for example, approximately amino acids 470-977 of humanIRE1 alpha); an effector domain from IRE1 beta (for example,approximately amino acids 452-925 of human IRE1 beta); an effectordomain from Nod1/CARD4 (for example, approximately amino acids 1-126 ofhuman Nod1/CARD4); an effector domain from Nod2 (for example,approximately amino acids 1-250 of human Nod2); an effector domain fromIpaf-1/CLAN/CARD12 (for example, approximately amino acids 1-125 ofhuman Ipaf-1/CLAN/CARD12); an acidic domain effector domain from CIITA(for example, approximately amino acids 1-340 of CARD-less human CIITA);a CARD effector domain from dendritic cell CIITA (for example,approximately amino acids 1-100 of human dendritic cell CIITA); aCARD-acidic-domain effector domain from dendritic cell CIITA (forexample, approximately amino acids 1-440 of human dendritic cell CIITA);an effector domain from IKK gamma (for example, full-length human IKKgamma or approximately amino acids 1-200 of human IKK gamma); aneffector domain from HSF1 (for example, approximately amino acids 1-227of human HSF1); an effector domain from RIP (for example, approximatelyamino acids 1-300 of human RIP); or an effector domain fromRip2/RICK/CARDIAK (for example, approximately amino acids 1-300 of humanRip2/RICK/CARDIAK).

In another preferred embodiment, the chimeric molecule or agent of theinvention has one or more apoptosis-signal-detection domains fromcaspase 9 (for example, approximately amino acids 1-92 of human caspase9), fused in frame with or bound to or associated with one or more ofthe following effector molecules: an apoptosis effector domain asdescribed supra; an effector domain from protein kinase R (for example,approximately amino acids 175-551 or 274-551 of human protein kinase R);an effector domain from RNase L (for example, approximately amino acids336-741 of human RNase L); an effector domain from PERK (for example,approximately amino acids 543-1115 of human PERK); an effector domainfrom IRE1 alpha (for example, approximately amino acids 470-977 of humanIRE1 alpha); an effector domain from IRE1 beta (for example,approximately amino acids 452-925 of human IRE1 beta); an effectordomain from Nod1/CARD4 (for example, approximately amino acids 1-126 ofhuman Nod1/CARD4); an effector domain from Nod2 (for example,approximately amino acids 1-250 of human Nod2); an effector domain fromIpaf-1/CLAN/CARD12 (for example, approximately amino acids 1-125 ofhuman Ipaf-1/CLAN/CARD12); an acidic domain effector domain from CIITA(for example, approximately amino acids 1-340 of CARD-less human CIITA);a CARD effector domain from dendritic cell CIITA (for example,approximately amino acids 1-100 of human dendritic cell CIITA); aCARD-acidic-domain effector domain from dendritic cell CIITA (forexample, approximately amino acids 1-440 of human dendritic cell CIITA);an effector domain from IKK gamma (for example, full-length human IKKgamma or approximately amino acids 1-200 of human IKK gamma); aneffector domain from HSF1 (for example, approximately amino acids 1-227of human HSF1); an effector domain from RIP (for example, approximatelyamino acids 1-300 of human RIP); or an effector domain fromRip2/RICK/CARDIAK (for example, approximately amino acids 1-300 of humanRip2/RICK/CARDIAK).

In another preferred embodiment, the chimeric molecule or agent of theinvention has one or more apoptosis-signal-detection domains from TNFalpha receptor 1 (for example, the extracellular and transmembranedomain of human TNF-RI), fused in frame with or bound to or associatedwith one or more of the following effector molecules: an apoptosiseffector domain as described supra; an effector domain from proteinkinase R (for example, approximately amino acids 175-551 or 274-551 ofhuman protein kinase R); an effector domain from RNase L (for example,approximately amino acids 336-741 of human RNase L); an effector domainfrom PERK (for example, approximately amino acids 543-1115 of humanPERK); an effector domain from IRE1 alpha (for example, approximatelyamino acids 470-977 of human IRE1 alpha); an effector domain from IRE1beta (for example, approximately amino acids 452-925 of human IRE1beta); an effector domain from Nod1/CARD4 (for example and withoutlimitation, approximately amino acids 1-126 of human Nod1/CARD4); aneffector domain from Nod2 (for example, approximately amino acids 1-250of human Nod2); an effector domain from Ipaf-1/CLAN/CARD12 (for example,approximately amino acids 1-125 of human Ipaf-1/CLAN/CARD12); an acidicdomain effector domain from CIITA (for example, approximately aminoacids 1-340 of CARD-less human CIITA); a CARD effector domain fromdendritic cell CIITA (for example, approximately amino acids 1-100 ofhuman dendritic cell CIITA); a CARD-acidic-domain effector domain fromdendritic cell CIITA (for example, approximately amino acids 1-440 ofhuman dendritic cell CIITA); an effector domain from IKK gamma (forexample, full-length human IKK gamma or approximately amino acids 1-200of human IKK gamma); an effector domain from HSF1 (for example,approximately amino acids 1-227 of human HSF1); an effector domain fromRIP (for example, approximately amino acids 1-300 of human RIP); or aneffector domain from Rip2/RICK/CARDIAK (for example, approximately aminoacids 1-300 of human Rip2/RICK/CARDIAK).

In another preferred embodiment, the chimeric molecule or agent of theinvention has one or more apoptosis-signal-detection domains fromFas/CD95 (for example, the extracellular and transmembrane domain ofhuman Fas/CD95), fused in frame with or bound to or associated with oneor more of the following effector molecules: an apoptosis effectordomain as described supra; an effector domain from protein kinase R (forexample, approximately amino acids 175-551 or 274-551 of human proteinkinase R); an effector domain from RNase L (for example, approximatelyamino acids 336-741 of human RNase L); an effector domain from PERK (forexample, approximately amino acids 543-1115 of human PERK); an effectordomain from IRE1 alpha (for example, approximately amino acids 470-977of human IRE1 alpha); an effector domain from IRE1 beta (for example,approximately amino acids 452-925 of human IRE1 beta); an effectordomain from Nod1/CARD4 (for example, approximately amino acids 1-126 ofhuman Nod1/CARD4); an effector domain from Nod2 (for example,approximately amino acids 1-250 of human Nod2); an effector domain fromIpaf-1/CLAN/CARD12 (for example, approximately amino acids 1-125 ofhuman Ipaf-1/CLAN/CARD12); an acidic domain effector domain from CIITA(for example, approximately amino acids 1-340 of CARD-less human CIITA);a CARD effector domain from dendritic cell CIITA (for example,approximately amino acids 1-100 of human dendritic cell CIITA); aCARD-acidic-domain effector domain from dendritic cell CIITA (forexample, approximately amino acids 1-440 of human dendritic cell CIITA);an effector domain from IKK gamma (for example, full-length human IKKgamma or approximately amino acids 1-200 of human IKK gamma); aneffector domain from HSF1 (for example, approximately amino acids 1-227of human HSF1); an effector domain from RIP (for example, approximatelyamino acids 1-300 of human RIP); or an effector domain fromRip2/RICK/CARDIAK (for example, approximately amino acids 1-300 of humanRip2/RICK/CARDIAK).

In another preferred embodiment, the chimeric molecule or agent of theinvention has one or more pathogen-detection domains from Nod1/CARD4(for example, approximately amino acids 127-953 of human Nod1/CARD4),fused in frame with or bound to or associated with one or more of thefollowing effector molecules: an apoptosis effector domain as describedsupra; an effector domain from protein kinase R (for example,approximately amino acids 175-551 or 274-551 of human protein kinase R);an effector domain from RNase L (for example, approximately amino acids336-741 of human RNase L); an effector domain from PERK (for example,approximately amino acids 543-1115 of human PERK); an effector domainfrom IRE1 alpha (for example, approximately amino acids 470-977 of humanIRE1 alpha); an effector domain from IRE1 beta (for example,approximately amino acids 452-925 of human IRE1 beta); an effectordomain from Nod2 (for example, approximately amino acids 1-250 of humanNod2); an effector domain from Ipaf-1/CLAN/CARD12 (for example,approximately amino acids 1-125 of human Ipaf-1/CLAN/CARD12); an acidicdomain effector domain from CIITA (for example, approximately aminoacids 1-340 of CARD-less human CIITA); a CARD effector domain fromdendritic cell CIITA (for example, approximately amino acids 1-100 ofhuman dendritic cell CIITA); a CARD-acidic-domain effector domain fromdendritic cell CIITA (for example, approximately amino acids 1-440 ofhuman dendritic cell CIITA); an effector domain from IKK gamma (forexample, full-length human IKK gamma or approximately amino acids 1-200of human IKK gamma); an effector domain from HSF1 (for example,approximately amino acids 1-227 of human HSF1); an effector domain fromRIP (for example, approximately amino acids 1-300 of human RIP); or aneffector domain from Rip2/RICK/CARDIAK (for example, approximately aminoacids 1-300 of human Rip2/RICK/CARDIAK).

In another preferred embodiment, the chimeric molecule or agent of theinvention has one or more pathogen-detection domains from Nod2 (forexample, approximately amino acids 251-1040 of human Nod2), fused inframe with or bound to or associated with one or more of the followingeffector molecules: an apoptosis effector domain as described supra; aneffector domain from protein kinase R (for example, approximately aminoacids 175-551 or 274-551 of human protein kinase R); an effector domainfrom RNase L (for example, approximately amino acids 336-741 of humanRNase L); an effector domain from PERK (for example, approximately aminoacids 543-1115 of human PERK); an effector domain from IRE1 alpha (forexample, approximately amino acids 470-977 of human IRE1 alpha); aneffector domain from IRE1 beta (for example, approximately amino acids452-925 of human IRE1 beta); an effector domain from Nod1/CARD4 (forexample, approximately amino acids 1-126 of human Nod1/CARD4); aneffector domain from Ipaf-1/CLAN/CARD12 (for example, approximatelyamino acids 1-125 of human Ipaf-1/CLAN/CARD12); an acidic domaineffector domain from CIITA (for example, approximately amino acids 1-340of CARD-less human CIITA); a CARD effector domain from dendritic cellCIITA (for example, approximately amino acids 1-100 of human dendriticcell CIITA); a CARD-acidic-domain effector domain from dendritic cellCIITA (for example, approximately amino acids 1-440 of human dendriticcell CIITA); an effector domain from IKK gamma (for example, full-lengthhuman IKK gamma or approximately amino acids 1-200 of human IKK gamma);an effector domain from HSF1 (for example, approximately amino acids1-227 of human HSF1); an effector domain from RIP (for example,approximately amino acids 1-300 of human RIP); or an effector domainfrom Rip2/RICK/CARDIAK (for example, approximately amino acids 1-300 ofhuman Rip2/RICK/CARDIAK).

In another preferred embodiment, the chimeric molecule or agent of theinvention has one or more pathogen-detection domains fromIpaf-1/CLAN/CARD12 (for example, approximately amino acids 126-1024 ofhuman Ipaf-1/CLAN/CARD12), fused in frame with or bound to or associatedwith one or more of the following effector molecules: an apoptosiseffector domain as described supra; an effector domain from proteinkinase R (for example, approximately amino acids 175-551 or 274-551 ofhuman protein kinase R); an effector domain from RNase L (for example,approximately amino acids 336-741 of human RNase L); an effector domainfrom PERK (for example, approximately amino acids 543-1115 of humanPERK); an effector domain from IRE1 alpha (for example, approximatelyamino acids 470-977 of human IRE1 alpha); an effector domain from IRE1beta (for example, approximately amino acids 452-925 of human IRE1beta); an effector domain from Nod1/CARD4 (for example, approximatelyamino acids 1-126 of human Nod1/CARD4); an effector domain from Nod2(for example, approximately amino acids 1-250 of human Nod2); an acidicdomain effector domain from CIITA (for example, approximately aminoacids 1-340 of CARD-less human CIITA); a CARD effector domain fromdendritic cell CIITA (for example, approximately amino acids 1-100 ofhuman dendritic cell CIITA); a CARD-acidic-domain effector domain fromdendritic cell CIITA (for example, approximately amino acids 1-440 ofhuman dendritic cell CIITA); an effector domain from IKK gamma (forexample, full-length human IKK gamma or approximately amino acids 1-200of human IKK gamma); an effector domain from HSF1 (for example,approximately amino acids 1-227 of human HSF1); an effector domain fromRIP (for example, approximately amino acids 1-300 of human RIP); or aneffector domain from Rip2/RICK/CARDIAK (for example, approximately aminoacids 1-300 of human Rip2/RICK/CARDIAK).

In another preferred embodiment, the chimeric molecule or agent of theinvention has one or more pathogen-detection domains from CIITA (forexample, approximately amino acids 341-1130 of CARD-less human CIITA),fused in frame with or bound to or associated with one or more of thefollowing effector molecules: an apoptosis effector domain as describedsupra; an effector domain from protein kinase R (for example,approximately amino acids 175-551 or 274-551 of human protein kinase R);an effector domain from RNase L (for example, approximately amino acids336-741 of human RNase L); an effector domain from PERK (for example,approximately amino acids 543-1115 of human PERK); an effector domainfrom IRE1 alpha (for example, approximately amino acids 470-977 of humanIRE1 alpha); an effector domain from IRE1 beta (for example,approximately amino acids 452-925 of human IRE1 beta); an effectordomain from Nod1/CARD4 (for example, approximately amino acids 1-126 ofhuman Nod1/CARD4); an effector domain from Nod2 (for example,approximately amino acids 1-250 of human Nod2); an effector domain fromIpaf-1/CLAN/CARD12 (for example, approximately amino acids 1-125 ofhuman Ipaf-1/CLAN/CARD12); an effector domain from IKK gamma (forexample, full-length human IKK gamma or approximately amino acids 1-200of human IKK gamma); an effector domain from HSF1 (for example,approximately amino acids 1-227 of human HSF1); an effector domain fromRIP (for example, approximately amino acids 1-300 of human RIP); or aneffector domain from Rip2/RICK/CARDIAK (for example, approximately aminoacids 1-300 of human Rip2/RICK/CARDIAK).

In another preferred embodiment, the chimeric molecule or agent of theinvention has one or more pathogen-binding domains orpathogen-induced-product-binding domains (for example, a single-chainantibody that binds to one or more pathogens, pathogen components,pathogen-produced products, or pathogen-induced products), fused inframe with or bound to or associated with one or more of the followingeffector molecules: an apoptosis effector domain as described supra; aneffector domain from protein kinase R (for example, approximately aminoacids 175-551 or 274-551 of human protein kinase R); an effector domainfrom RNase L (for example, approximately amino acids 336-741 of humanRNase L); an effector domain from PERK (for example, approximately aminoacids 543-1115 of human PERK); an effector domain from IRE1 alpha (forexample, approximately amino acids 470-977 of human IRE1 alpha); aneffector domain from IRE1 beta (for example, approximately amino acids452-925 of human IRE1 beta); an effector domain from Nod1/CARD4 (forexample, approximately amino acids 1-126 of human Nod1/CARD4); aneffector domain from Nod2 (for example, approximately amino acids 1-250of human Nod2); an effector domain from Ipaf-1/CLAN/CARD12 (for example,approximately amino acids 1-125 of human Ipaf-1/CLAN/CARD12); an acidicdomain effector domain from CIITA (for example, approximately aminoacids 1-340 of CARD-less human CIITA); a CARD effector domain fromdendritic cell CIITA (for example, approximately amino acids 1-100 ofhuman dendritic cell CIITA); a CARD-acidic-domain effector domain fromdendritic cell CIITA (for example, approximately amino acids 1-440 ofhuman dendritic cell CIITA); an effector domain from IKK gamma (forexample, full-length human IKK gamma or approximately amino acids 1-200of human IKK gamma); an effector domain from HSF1 (for example,approximately amino acids 1-227 of human HSF1); a protease that isactivated by crosslinking; an effector domain from RIP (for example,approximately amino acids 1-300 of human RIP); or an effector domainfrom Rip2/RICK/CARDIAK (for example, approximately amino acids 1-300 ofhuman Rip2/RICK/CARDIAK).

In another preferred embodiment, the chimeric molecule or agent of theinvention has one or more domains that specifically bind to one or morepathogenic forms of prions (for example, a portion of a nonpathogenicprion form (such as approximately amino acids 119-136 of hamster prionprotein; J. Chabry et al. (1999) Journal of Virology 73, 6245-6250) thatbinds to a pathogenic prion form, or a single-chain antibody that bindsto one or more pathogenic forms of prions), fused in frame with or boundto or associated with one or more of the following effector molecules:an effector domain from protein kinase R (for example, approximatelyamino acids 175-551 or 274-551 of human protein kinase R); an effectordomain from RNase L (for example, approximately amino acids 336-741 ofhuman RNase L); an effector domain from PERK (for example, approximatelyamino acids 543-1115 of human PERK); an effector domain from IRE1 alpha(for example, approximately amino acids 470-977 of human IRE1 alpha); aneffector domain from IRE1 beta (for example, approximately amino acids452-925 of human IRE1 beta); an effector domain from HSF1 (for example,approximately amino acids 1-227 of human HSF1); an effector domain fromNod1/CARD4 (for example, approximately amino acids 1-126 of humanNod1/CARD4); an effector domain from Nod2 (for example, approximatelyamino acids 1-250 of human Nod2); an effector domain fromIpaf-1/CLAN/CARD12 (for example, approximately amino acids 1-125 ofhuman Ipaf-1/CLAN/CARD12); an acidic domain effector domain from CIITA(for example, approximately amino acids 1-340 of CARD-less human CIITA);a CARD effector domain from dendritic cell CIITA (for example,approximately amino acids 1-100 of human dendritic cell CIITA); aCARD-acidic-domain effector domain from dendritic cell CIITA (forexample, approximately amino acids 1-440 of human dendritic cell CIITA);an effector domain from IKK gamma (for example, full-length human IKKgamma or approximately amino acids 1-200 of human IKK gamma); a proteasethat is activated by crosslinking; an effector domain from RIP (forexample, approximately amino acids 1-300 of human RIP); or an effectordomain from Rip2/RICK/CARDIAK (for example, approximately amino acids1-300 of human Rip2/RICK/CARDIAK).

In another preferred embodiment, the chimeric molecule or agent of theinvention has one or more inflammatory-signal-detection domains from IKKgamma (for example, full-length human IKK gamma), fused in frame with orbound to or associated with one or more of the following effectormolecules: an apoptosis effector domain as described supra; an effectordomain from protein kinase R (for example, approximately amino acids175-551 or 274-551 of human protein kinase R); an effector domain fromRNase L (for example, approximately amino acids 336-741 of human RNaseL); an effector domain from PERK (for example, approximately amino acids543-1115 of human PERK); an effector domain from IRE1 alpha (forexample, approximately amino acids 470-977 of human IRE1 alpha); aneffector domain from IRE1 beta (for example, approximately amino acids452-925 of human IRE1 beta); an effector domain from Nod1/CARD4 (forexample, approximately amino acids 1-126 of human Nod1/CARD4); aneffector domain from Nod2 (for example, approximately amino acids 1-250of human Nod2); an effector domain from Ipaf-1/CLAN/CARD12 (for example,approximately amino acids 1-125 of human Ipaf-1/CLAN/CARD12); an acidicdomain effector domain from CIITA (for example, approximately aminoacids 1-340 of CARD-less human CIITA); a CARD effector domain fromdendritic cell CIITA (for example, approximately amino acids 1-100 ofhuman dendritic cell CIITA); a CARD-acidic-domain effector domain fromdendritic cell CIITA (for example, approximately amino acids 1-440 ofhuman dendritic cell CIITA); an effector domain from HSF1 (for example,approximately amino acids 1-227 of human HSF1); an effector domain fromRIP (for example, approximately amino acids 1-300 of human RIP); or aneffector domain from Rip2/RICK/CARDIAK (for example, approximately aminoacids 1-300 of human Rip2/RICK/CARDIAK).

In another preferred embodiment, the chimeric molecule or agent of theinvention has one or more pathogen-induced-signal-detection domains fromRIP (for example, approximately amino acids 301-671 of human RIP), fusedin frame with or bound to or associated with one or more of thefollowing effector molecules: an apoptosis effector domain as describedsupra; an effector domain from protein kinase R (for example,approximately amino acids 175-551 or 274-551 of human protein kinase R);an effector domain from RNase L (for example, approximately amino acids336-741 of human RNase L); an effector domain from PERK (for example,approximately amino acids 543-1115 of human PERK); an effector domainfrom IRE1 alpha (for example, approximately amino acids 470-977 of humanIRE1 alpha); an effector domain from IRE1 beta (for example,approximately amino acids 452-925 of human IRE1 beta); an effectordomain from Nod1/CARD4 (for example, approximately amino acids 1-126 ofhuman Nod1/CARD4); an effector domain from Nod2 (for example,approximately amino acids 1-250 of human Nod2); an effector domain fromIpaf-1/CLAN/CARD12 (for example, approximately amino acids 1-125 ofhuman Ipaf-1/CLAN/CARD12); an acidic domain effector domain from CIITA(for example, approximately amino acids 1-340 of CARD-less human CIITA);a CARD effector domain from dendritic cell CIITA (for example,approximately amino acids 1-100 of human dendritic cell CIITA); aCARD-acidic-domain effector domain from dendritic cell CIITA (forexample, approximately amino acids 1-440 of human dendritic cell CIITA);an effector domain from IKK gamma (for example, full-length human IKKgamma or approximately amino acids 1-200 of human IKK gamma); aneffector domain from HSF1 (for example, approximately amino acids 1-227of human HSF1); or an effector domain from Rip2/RICK/CARDIAK (forexample, approximately amino acids 1-300 of human Rip2/RICK/CARDIAK).

In another preferred embodiment, the chimeric molecule or agent of theinvention has one or more pathogen-induced-signal-detection domains fromRip2/RICK/CARDIAK (for example, approximately amino acids 301-540 ofhuman Rip2/RICK/CARDIAK), fused in frame with or bound to or associatedwith one or more of the following effector molecules: an apoptosiseffector domain as described supra; an effector domain from proteinkinase R (for example, approximately amino acids 175-551 or 274-551 ofhuman protein kinase R); an effector domain from RNase L (for example,approximately amino acids 336-741 of human RNase L); an effector domainfrom PERK (for example, approximately amino acids 543-1115 of humanPERK); an effector domain from IRE1 alpha (for example, approximatelyamino acids 470-977 of human IRE1 alpha); an effector domain from IRE1beta (for example, approximately amino acids 452-925 of human IRE1beta); an effector domain from Nod1/CARD4 (for example, approximatelyamino acids 1-126 of human Nod1/CARD4); an effector domain from Nod2(for example, approximately amino acids 1-250 of human Nod2); aneffector domain from Ipaf-1/CLAN/CARD12 (for example, approximatelyamino acids 1-125 of human Ipaf-1/CLAN/CARD12); an acidic domaineffector domain from CIITA (for example, approximately amino acids 1-340of CARD-less human CIITA); a CARD effector domain from dendritic cellCIITA (for example, approximately amino acids 1-100 of human dendriticcell CIITA); a CARD-acidic-domain effector domain from dendritic cellCIITA (for example, approximately amino acids 1-440 of human dendriticcell CIITA); an effector domain from IKK gamma (for example, full-lengthhuman IKK gamma or approximately amino acids 1-200 of human IKK gamma);an effector domain from HSF1 (for example, approximately amino acids1-227 of human HSF1); or an effector domain from RIP (for example,approximately amino acids 1-300 of human RIP).

In another preferred embodiment, the chimeric molecule or agent of theinvention has one or more pathogen-detection domains isolated fromtoll-like receptors (for example, the extracellular domain of thefollowing human toll-like receptors: TLR1, TLR2, TLR3, TLR4, TLR5, TLR6,TLR7, TLR8, TLR9, or TLR10), fused in frame with or bound to orassociated with one or more of the following effector molecules: anapoptosis effector domain as described supra; an effector domain fromprotein kinase R (for example, approximately amino acids 175-551 or274-551 of human protein kinase R); an effector domain from RNase L (forexample, approximately amino acids 336-741 of human RNase L); aneffector domain from PERK (for example, approximately amino acids543-1115 of human PERK); an effector domain from IRE1 alpha (forexample, approximately amino acids 470-977 of human IRE1 alpha); aneffector domain from IRE1 beta (for example, approximately amino acids452-925 of human IRE1 beta); an effector domain from Nod1/CARD4 (forexample, approximately amino acids 1-126 of human Nod1/CARD4); aneffector domain from Nod2 (for example, approximately amino acids 1-250of human Nod2); an effector domain from Ipaf-1/CLAN/CARD12 (for example,approximately amino acids 1-125 of human Ipaf-1/CLAN/CARD12); an acidicdomain effector domain from CIITA (for example, approximately aminoacids 1-340 of CARD-less human CIITA); a CARD effector domain fromdendritic cell CIITA (for example, approximately amino acids 1-100 ofhuman dendritic cell CIITA); a CARD-acidic-domain effector domain fromdendritic cell CIITA (for example, approximately amino acids 1-440 ofhuman dendritic cell CIITA); an effector domain from IKK gamma (forexample, full-length human IKK gamma or approximately amino acids 1-200of human IKK gamma); an effector domain from HSF1 (for example,approximately amino acids 1-227 of human HSF1); an effector domain fromRIP (for example, approximately amino acids 1-300 of human RIP); or aneffector domain from Rip2/RICK/CARDIAK (for example, approximately aminoacids 1-300 of human Rip2/RICK/CARDIAK).

A chimeric molecule or agent of the invention can be a molecule thatbinds to a pathogen or a product produced or induced by a pathogen andthat also binds to a natural effector molecule, thereby activatingeffector molecules by crosslinking on a polyvalentpathogen/pathogen-produced product/pathogen-induced product and/orpromoting an anti-pathogen effect by bringing apathogen/pathogen-produced product into close proximity with a naturalanti-pathogen effector molecule. More specifically, and withoutrestriction, an agent of the invention can be a molecule that binds to apathogen or product produced or induced by a pathogen and that alsobinds to one or more of the following: protein kinase R (for example, bybinding within the domain from approximately amino acids 1-174 of humanprotein kinase R); RNase L (for example, by containing or by mimicking ashort molecule of 2′,5′-oligoadenylate that binds to RNase L but doesnot activate it without a secondary crosslinker, which in this case is apathogen or a product produced or induced by a pathogen); PERK; IRE1alpha; IRE1 beta; caspase 3; caspase 8 (for example, by mimicking thecaspase-8-binding DED domain from approximately amino acids 1-117 ofhuman FADD); caspase 9 (for example, by mimicking the caspase-9-bindingCARD domain from approximately amino acids 1-97 of human Apaf-1);Apaf-1; FADD (for example, by mimicking the death domain (DD) from humanFas/CD95 or TRADD); a caspase or apoptosis signaling molecule;Nod1/CARD4 (for example, by binding within the domain from approximatelyamino acids 126-953 of human Nod1/CARD4); Nod2 (for example, by bindingwithin the domain from approximately amino acids 220-1040 of humanNod2); Ipaf-1/CLAN/CARD12 (for example, by binding within the domainfrom approximately amino acids 125-1024 of human Ipaf-1/CLAN/CARD12);CIITA (for example, by binding within the nucleotide oligomerizationdomain (NOD) or leucine-rich-repeat (LRR) domain of a CIITA isoform);RIP (for example, by mimicking the death domain (DD) of Fas/CD95 orTRADD); Rip2/RICK/CARDIAK (for example, by mimicking the CARD domainfrom approximately amino acids 1-126 of human Nod1); IKK gamma (forexample, by binding with the domain from approximately amino acids201-419 of human IKK gamma); IKK alpha and/or beta (for example, bymimicking the IKK alpha/beta binding domain from approximately aminoacids 1-200 of human IKK gamma); HSF1 (for example, by binding withinthe domain from approximately amino acids 137-503 of human HSF1); aDNase as described supra; an RNase as described supra; a protease asdescribed supra; a protease that is activated by crosslinking; aglycosidase as described supra; a lipase as described supra; a heatshock protein as described supra; an E3 ubiquitin ligase as describedsupra.

A chimeric molecule or agent of the invention can be a molecule thatbinds to dsRNA (for example, by containing lividomycin or by mimickingthe dsRNA-binding domain of lividomycin, protein kinase R, or otherdsRNA-binding domains as described supra) and that also binds to one ormore of the following: protein kinase R (for example, by binding withinthe domain from approximately amino acids 1-174 of human protein kinaseR); RNase L (for example, by containing or by mimicking a short moleculeof 2′,5′-oligoadenylate that binds to RNase L but does not activate itwithout a secondary crosslinker, which in this case is a pathogen or aproduct produced or induced by a pathogen); PERK; IRE1 alpha; IRE1 beta;caspase 3; caspase 8 (for example, by mimicking the caspase-8-bindingDED domain from approximately amino acids 1-117 of human FADD); caspase9 (for example, by mimicking the caspase-9-binding CARD domain fromapproximately amino acids 1-97 of human Apaf-1); Apaf-1; FADD (forexample, by mimicking the death domain (DD) from human Fas/CD95 orTRADD); a caspase or apoptosis signaling molecule; Nod1/CARD4 (forexample, by binding within the domain from approximately amino acids126-953 of human Nod1/CARD4); Nod2 (for example, by binding within thedomain from approximately amino acids 220-1040 of human Nod2);Ipaf-1/CLAN/CARD12 (for example, by binding within the domain fromapproximately amino acids 125-1024 of human Ipaf-1/CLAN/CARD12); CIITA(for example, by binding within the nucleotide oligomerization domain(NOD) or leucine-rich-repeat (LRR) domain of a CIITA isoform); RIP (forexample, by mimicking the death domain (DD) of Fas/CD95 or TRADD);Rip2/RICK/CARDIAK (for example, by mimicking the CARD domain fromapproximately amino acids 1-126 of human Nod1); IKK gamma (for example,by binding with the domain from approximately amino acids 201-419 ofhuman IKK gamma); IKK alpha and/or beta (for example, by mimicking theIKK alpha/beta binding domain from approximately amino acids 1-200 ofhuman IKK gamma); HSF1 (for example, by binding within the domain fromapproximately amino acids 137-503 of human HSF1); a DNase as describedsupra; an RNase as described supra; a protease as described supra; aglycosidase as described supra; a lipase as described supra; a heatshock protein as described supra; an E3 ubiquitin ligase as describedsupra.

A chimeric molecule or agent of the invention can be a molecule thatbinds to protein kinase R (for example, by binding within the domainfrom approximately amino acids 174-551 of human protein kinase R) andthat also binds to one or more of the following: RNase L (for example,by containing or by mimicking a short molecule of 2′,5′-oligoadenylatethat binds to RNase L but does not activate it without a secondarycrosslinker, which in this case is a pathogen or a product produced orinduced by a pathogen); PERK; IRE1 alpha; IRE1 beta; caspase 3; caspase8 (for example, by mimicking the caspase-8-binding DED domain fromapproximately amino acids 1-117 of human FADD); caspase 9 (for example,by mimicking the caspase-9-binding CARD domain from approximately aminoacids 1-97 of human Apaf-1); Apaf-1; FADD (for example, by mimicking thedeath domain (DD) from human Fas/CD95 or TRADD); a caspase or apoptosissignaling molecule; Nod1/CARD4 (for example, by binding within thedomain from approximately amino acids 126-953 of human Nod1/CARD4); Nod2(for example, by binding within the domain from approximately aminoacids 220-1040 of human Nod2); Ipaf-1/CLAN/CARD12 (for example, bybinding within the domain from approximately amino acids 125-1024 ofhuman Ipaf-1/CLAN/CARD12); CIITA (for example, by binding within thenucleotide oligomerization domain (NOD) or leucine-rich-repeat (LRR)domain of a CIITA isoform); RIP (for example, by mimicking the deathdomain (DD) of Fas/CD95 or TRADD); Rip2/RICK/CARDIAK (for example, bymimicking the CARD domain from approximately amino acids 1-126 of humanNod1); IKK gamma (for example, by binding with the domain fromapproximately amino acids 201-419 of human IKK gamma); IKK alpha and/orbeta (for example, by mimicking the IKK alpha/beta binding domain fromapproximately amino acids 1-200 of human IKK gamma); HSF1 (for example,by binding within the domain from approximately amino acids 137-503 ofhuman HSF1); a DNase as described supra; an RNase as described supra; aprotease as described supra; a glycosidase as described supra; a lipaseas described supra; a heat shock protein as described supra; an E3ubiquitin ligase as described supra.

A chimeric molecule or agent of the invention can be a molecule thatbinds to 2′,5′-oligoadenylate (for example, by mimicking the2′,5′-oligoadenylate-binding domain from approximately amino acids 1-335of human RNase L) and that also binds to one or more of the following:protein kinase R (for example, by binding within the domain fromapproximately amino acids 1-174 of human protein kinase R); RNase L (forexample, by containing or by mimicking a short molecule of2′,5′-oligoadenylate that binds to RNase L but does not activate itwithout a secondary crosslinker, which in this case is a pathogen or aproduct produced or induced by a pathogen); PERK; IRE1 alpha; IRE1 beta;caspase 3; caspase 8 (for example, by mimicking the caspase-8-bindingDED domain from approximately amino acids 1-117 of human FADD); caspase9 (for example, by mimicking the caspase-9-binding CARD domain fromapproximately amino acids 1-97 of human Apaf-1); Apaf-1; FADD (forexample, by mimicking the death domain (DD) from human Fas/CD95 orTRADD); a caspase or apoptosis signaling molecule; Nod1/CARD4 (forexample, by binding within the domain from approximately amino acids126-953 of human Nod1/CARD4); Nod2 (for example, by binding within thedomain from approximately amino acids 220-1040 of human Nod2);Ipaf-1/CLAN/CARD12 (for example, by binding within the domain fromapproximately amino acids 125-1024 of human Ipaf-1/CLAN/CARD12); CIITA(for example, by binding within the nucleotide oligomerization domain(NOD) or leucine-rich-repeat (LRR) domain of a CIITA isoform); RIP (forexample, by mimicking the death domain (DD) of Fas/CD95 or TRADD);Rip2/RICK/CARDIAK (for example, by mimicking the CARD domain fromapproximately amino acids 1-126 of human Nod1); IKK gamma (for example,by binding with the domain from approximately amino acids 201-419 ofhuman IKK gamma); IKK alpha and/or beta (for example, by mimicking theIKK alpha/beta binding domain from approximately amino acids 1-200 ofhuman IKK gamma); HSF1 (for example, by binding within the domain fromapproximately amino acids 137-503 of human HSF1); a DNase as describedsupra; an RNase as described supra; a protease as described supra; aglycosidase as described supra; a lipase as described supra; a heatshock protein as described supra; an E3 ubiquitin ligase as describedsupra.

A chimeric molecule or agent of the invention can be a molecule thatbinds to RNase L (for example, by binding within the domain fromapproximately amino acids 364-741 of human RNase L) and that also bindsto one or more of the following: protein kinase R (for example, bybinding within the domain from approximately amino acids 1-174 of humanprotein kinase R); PERK; IRE1 alpha; IRE1 beta; caspase 3; caspase 8(for example, by mimicking the caspase-8-binding DED domain fromapproximately amino acids 1-117 of human FADD); caspase 9 (for example,by mimicking the caspase-9-binding CARD domain from approximately aminoacids 1-97 of human Apaf-1); Apaf-1; FADD (for example, by mimicking thedeath domain (DD) from human Fas/CD95 or TRADD); a caspase or apoptosissignaling molecule; Nod1/CARD4 (for example, by binding within thedomain from approximately amino acids 126-953 of human Nod1/CARD4); Nod2(for example, by binding within the domain from approximately aminoacids 220-1040 of human Nod2); Ipaf-1/CLAN/CARD12 (for example, bybinding within the domain from approximately amino acids 125-1024 ofhuman Ipaf-1/CLAN/CARD12); CIITA (for example, by binding within thenucleotide oligomerization domain (NOD) or leucine-rich-repeat (LRR)domain of a CIITA isoform); RIP (for example, by mimicking the deathdomain (DD) of Fas/CD95 or TRADD); Rip2/RICK/CARDIAK (for example, bymimicking the CARD domain from approximately amino acids 1-126 of humanNod1); IKK gamma (for example, by binding with the domain fromapproximately amino acids 201-419 of human IKK gamma); IKK alpha and/orbeta (for example, by mimicking the IKK alpha/beta binding domain fromapproximately amino acids 1-200 of human IKK gamma); HSF1 (for example,by binding within the domain from approximately amino acids 137-503 ofhuman HSF1); a DNase as described supra; an RNase as described supra; aprotease as described supra; a glycosidase as described supra; a lipaseas described supra; a heat shock protein as described supra; an E3ubiquitin ligase as described supra.

A chimeric molecule or agent of the invention can be a molecule thatbinds to viral late domains (for example and without restriction, bybinding to viral late domain motifs such as PTAP, PSAP, PPXY, YPDL, orYXXL, as described supra) and that also binds to one or more of thefollowing: protein kinase R (for example, by binding within the domainfrom approximately amino acids 1-174 of human protein kinase R); RNase L(for example, by containing or by mimicking a short molecule of2′,5′-oligoadenylate that binds to RNase L but does not activate itwithout a secondary crosslinker, which in this case is a pathogen or aproduct produced or induced by a pathogen); PERK; IRE1 alpha; IRE1 beta;caspase 3; caspase 8 (for example, by mimicking the caspase-8-bindingDED domain from approximately amino acids 1-117 of human FADD); caspase9 (for example, by mimicking the caspase-9-binding CARD domain fromapproximately amino acids 1-97 of human Apaf-1); Apaf-1; FADD (forexample, by mimicking the death domain (DD) from human Fas/CD95 orTRADD); a caspase or apoptosis signaling molecule; Nod1/CARD4 (forexample, by binding within the domain from approximately amino acids126-953 of human Nod1/CARD4); Nod2 (for example, by binding within thedomain from approximately amino acids 220-1040 of human Nod2);Ipaf-1/CLAN/CARD12 (for example, by binding within the domain fromapproximately amino acids 125-1024 of human Ipaf-1/CLAN/CARD12); CIITA(for example, by binding within the nucleotide oligomerization domain(NOD) or leucine-rich-repeat (LRR) domain of a CIITA isoform); RIP (forexample, by mimicking the death domain (DD) of Fas/CD95 or TRADD);Rip2/RICK/CARDIAK (for example, by mimicking the CARD domain fromapproximately amino acids 1-126 of human Nod1); IKK gamma (for example,by binding with the domain from approximately amino acids 201-419 ofhuman IKK gamma); IKK alpha and/or beta (for example, by mimicking theIKK alpha/beta binding domain from approximately amino acids 1-200 ofhuman IKK gamma); HSF1 (for example, by binding within the domain fromapproximately amino acids 137-503 of human HSF1); a DNase as describedsupra; an RNase as described supra; a protease as described supra; aglycosidase as described supra; a lipase as described supra; a heatshock protein as described supra; an E3 ubiquitin ligase as describedsupra.

A chimeric molecule or agent of the invention can be a molecule thatbinds to viral glycoproteins (for example and without restriction, bymimicking the hemagglutinin-binding domain of human NK cell activationreceptor NKp46) and that also binds to one or more of the following:protein kinase R (for example, by binding within the domain fromapproximately amino acids 1-174 of human protein kinase R); RNase L (forexample, by containing or by mimicking a short molecule of2′,5′-oligoadenylate that binds to RNase L but does not activate itwithout a secondary crosslinker, which in this case is a pathogen or aproduct produced or induced by a pathogen); PERK; IRE1 alpha; IRE1 beta;caspase 3; caspase 8 (for example, by mimicking the caspase-8-bindingDED domain from approximately amino acids 1-117 of human FADD); caspase9 (for example, by mimicking the caspase-9-binding CARD domain fromapproximately amino acids 1-97 of human Apaf-1); Apaf-1; FADD (forexample, by mimicking the death domain (DD) from human Fas/CD95 orTRADD); a caspase or apoptosis signaling molecule; Nod1/CARD4 (forexample, by binding within the domain from approximately amino acids126-953 of human Nod1/CARD4); Nod2 (for example, by binding within thedomain from approximately amino acids 220-1040 of human Nod2);Ipaf-1/CLAN/CARD12 (for example, by binding within the domain fromapproximately amino acids 125-1024 of human Ipaf-1/CLAN/CARD12); CIITA(for example, by binding within the nucleotide oligomerization domain(NOD) or leucine-rich-repeat (LRR) domain of a CIITA isoform); RIP (forexample, by mimicking the death domain (DD) of Fas/CD95 or TRADD);Rip2/RICK/CARDIAK (for example, by mimicking the CARD domain fromapproximately amino acids 1-126 of human Nod1); IKK gamma (for example,by binding with the domain from approximately amino acids 201-419 ofhuman IKK gamma); IKK alpha and/or beta (for example, by mimicking theIKK alpha/beta binding domain from approximately amino acids 1-200 ofhuman IKK gamma); HSF1 (for example, by binding within the domain fromapproximately amino acids 137-503 of human HSF1); a DNase as describedsupra; an RNase as described supra; a protease as described supra; aglycosidase as described supra; a lipase as described supra; a heatshock protein as described supra; an E3 ubiquitin ligase as describedsupra.

A chimeric molecule or agent of the invention can be a molecule thatbinds to LPS (for example, by mimicking the LPS-binding domain fromapproximately amino acids 1-199 of human BPI or other LPS-bindingdomains as described supra) and that also binds to one or more of thefollowing: protein kinase R (for example, by binding within the domainfrom approximately amino acids 1-174 of human protein kinase R); RNase L(for example, by containing or by mimicking a short molecule of2′,5′-oligoadenylate that binds to RNase L but does not activate itwithout a secondary crosslinker, which in this case is a pathogen or aproduct produced or induced by a pathogen); PERK; IRE1 alpha; IRE1 beta;caspase 3; caspase 8 (for example, by mimicking the caspase-8-bindingDED domain from approximately amino acids 1-117 of human FADD); caspase9 (for example, by mimicking the caspase-9-binding CARD domain fromapproximately amino acids 1-97 of human Apaf-1); Apaf-1; FADD (forexample, by mimicking the death domain (DD) from human Fas/CD95 orTRADD); a caspase or apoptosis signaling molecule; Nod1/CARD4 (forexample, by binding within the domain from approximately amino acids126-953 of human Nod1/CARD4); Nod2 (for example, by binding within thedomain from approximately amino acids 220-1040 of human Nod2);Ipaf-1/CLAN/CARD12 (for example, by binding within the domain fromapproximately amino acids 125-1024 of human Ipaf-1/CLAN/CARD12); CIITA(for example, by binding within the nucleotide oligomerization domain(NOD) or leucine-rich-repeat (LRR) domain of a CIITA isoform); RIP (forexample, by mimicking the death domain (DD) of Fas/CD95 or TRADD);Rip2/RICK/CARDIAK (for example, by mimicking the CARD domain fromapproximately amino acids 1-126 of human Nod1); IKK gamma (for example,by binding with the domain from approximately amino acids 201-419 ofhuman IKK gamma); IKK alpha and/or beta (for example, by mimicking theIKK alpha/beta binding domain from approximately amino acids 1-200 ofhuman IKK gamma); HSF1 (for example, by binding within the domain fromapproximately amino acids 137-503 of human HSF1); a DNase as describedsupra; an RNase as described supra; a protease as described supra; aglycosidase as described supra; a lipase as described supra; a heatshock protein as described supra; an E3 ubiquitin ligase as describedsupra.

A chimeric molecule or agent of the invention can be a molecule thatbinds to peptidoglycan (for example, by mimicking thepeptidoglycan-binding domain from the extracellular domain of humanTLR2) and that also binds to one or more of the following: proteinkinase R (for example, by binding within the domain from approximatelyamino acids 1-174 of human protein kinase R); RNase L (for example, bycontaining or by mimicking a short molecule of 2′,5′-oligoadenylate thatbinds to RNase L but does not activate it without a secondarycrosslinker, which in this case is a pathogen or a product produced orinduced by a pathogen); PERK; IRE1 alpha; IRE1 beta; caspase 3; caspase8 (for example, by mimicking the caspase-8-binding DED domain fromapproximately amino acids 1-117 of human FADD); caspase 9 (for example,by mimicking the caspase-9-binding CARD domain from approximately aminoacids 1-97 of human Apaf-1); Apaf-1; FADD (for example, by mimicking thedeath domain (DD) from human Fas/CD95 or TRADD); a caspase or apoptosissignaling molecule; Nod1/CARD4 (for example, by binding within thedomain from approximately amino acids 126-953 of human Nod1/CARD4); Nod2(for example, by binding within the domain from approximately aminoacids 220-1040 of human Nod2); Ipaf-1/CLAN/CARD12 (for example, bybinding within the domain from approximately amino acids 125-1024 ofhuman Ipaf-1/CLAN/CARD12); CIITA (for example, by binding within thenucleotide oligomerization domain (NOD) or leucine-rich-repeat (LRR)domain of a CIITA isoform); RIP (for example, by mimicking the deathdomain (DD) of Fas/CD95 or TRADD); Rip2/RICK/CARDIAK (for example, bymimicking the CARD domain from approximately amino acids 1-126 of humanNod1); IKK gamma (for example, by binding with the domain fromapproximately amino acids 201-419 of human IKK gamma); IKK alpha and/orbeta (for example, by mimicking the IKK alpha/beta binding domain fromapproximately amino acids 1-200 of human IKK gamma); HSF1 (for example,by binding within the domain from approximately amino acids 137-503 ofhuman HSF1); a DNase as described supra; an RNase as described supra; aprotease as described supra; a glycosidase as described supra; a lipaseas described supra; a heat shock protein as described supra; an E3ubiquitin ligase as described supra.

A chimeric molecule or agent of the invention can be a molecule thatbinds to muramyl dipeptide (for example, by mimicking themuramyl-dipeptide-binding domain from approximately amino acids 744-1040of human Nod2) and that also binds to one or more of the following:protein kinase R (for example, by binding within the domain fromapproximately amino acids 1-174 of human protein kinase R); RNase L (forexample, by containing or by mimicking a short molecule of2′,5′-oligoadenylate that binds to RNase L but does not activate itwithout a secondary crosslinker, which in this case is a pathogen or aproduct produced or induced by a pathogen); PERK; IRE1 alpha; IRE1 beta;caspase 3; caspase 8 (for example, by mimicking the caspase-8-bindingDED domain from approximately amino acids 1-117 of human FADD); caspase9 (for example, by mimicking the caspase-9-binding CARD domain fromapproximately amino acids 1-97 of human Apaf-1); Apaf-1; FADD (forexample, by mimicking the death domain (DD) from human Fas/CD95 orTRADD); a caspase or apoptosis signaling molecule; Nod1/CARD4 (forexample, by binding within the domain from approximately amino acids126-953 of human Nod1/CARD4); Nod2 (for example, by binding within thedomain from approximately amino acids 220-1040 of human Nod2);Ipaf-1/CLAN/CARD12 (for example, by binding within the domain fromapproximately amino acids 125-1024 of human Ipaf-1/CLAN/CARD12); CIITA(for example, by binding within the nucleotide oligomerization domain(NOD) or leucine-rich-repeat (LRR) domain of a CIITA isoform); RIP (forexample, by mimicking the death domain (DD) of Fas/CD95 or TRADD);Rip2/RICK/CARDIAK (for example, by mimicking the CARD domain fromapproximately amino acids 1-126 of human Nod1); IKK gamma (for example,by binding with the domain from approximately amino acids 201-419 ofhuman IKK gamma); IKK alpha and/or beta (for example, by mimicking theIKK alpha/beta binding domain from approximately amino acids 1-200 ofhuman IKK gamma); HSF1 (for example, by binding within the domain fromapproximately amino acids 137-503 of human HSF1); a DNase as describedsupra; an RNase as described supra; a protease as described supra; aglycosidase as described supra; a lipase as described supra; a heatshock protein as described supra; an E3 ubiquitin ligase as describedsupra.

A chimeric molecule or agent of the invention can be a molecule thatbinds to bacterial flagellin (for example, by mimicking theflagellin-binding domain from the extracellular domain of human TLR5)and that also binds to one or more of the following: protein kinase R(for example, by binding within the domain from approximately aminoacids 1-174 of human protein kinase R); RNase L (for example, bycontaining or by mimicking a short molecule of 2′,5′-oligoadenylate thatbinds to RNase L but does not activate it without a secondarycrosslinker, which in this case is a pathogen or a product produced orinduced by a pathogen); PERK; IRE1 alpha; IRE1 beta; caspase 3; caspase8 (for example, by mimicking the caspase-8-binding DED domain fromapproximately amino acids 1-117 of human FADD); caspase 9 (for example,by mimicking the caspase-9-binding CARD domain from approximately aminoacids 1-97 of human Apaf-1); Apaf-1; FADD (for example, by mimicking thedeath domain (DD) from human Fas/CD95 or TRADD); a caspase or apoptosissignaling molecule; Nod1/CARD4 (for example, by binding within thedomain from approximately amino acids 126-953 of human Nod1/CARD4); Nod2(for example, by binding within the domain from approximately aminoacids 220-1040 of human Nod2); Ipaf-1/CLAN/CARD12 (for example, bybinding within the domain from approximately amino acids 125-1024 ofhuman Ipaf-1/CLAN/CARD12); CIITA (for example, by binding within thenucleotide oligomerization domain (NOD) or leucine-rich-repeat (LRR)domain of a CIITA isoform); RIP (for example, by mimicking the deathdomain (DD) of Fas/CD95 or TRADD); Rip2/RICK/CARDIAK (for example, bymimicking the CARD domain from approximately amino acids 1-126 of humanNod1); IKK gamma (for example, by binding with the domain fromapproximately amino acids 201-419 of human IKK gamma); IKK alpha and/orbeta (for example, by mimicking the IKK alpha/beta binding domain fromapproximately amino acids 1-200 of human IKK gamma); HSF1 (for example,by binding within the domain from approximately amino acids 137-503 ofhuman HSF1); a DNase as described supra; an RNase as described supra; aprotease as described supra; a glycosidase as described supra; a lipaseas described supra; a heat shock protein as described supra; an E3ubiquitin ligase as described supra.

A chimeric molecule or agent of the invention can be a molecule thatbinds to a bacterial type III secretion system and that also binds toone or more of the following: protein kinase R (for example, by bindingwithin the domain from approximately amino acids 1-174 of human proteinkinase R); RNase L (for example, by containing or by mimicking a shortmolecule of 2′,5′-oligoadenylate that binds to RNase L but does notactivate it without a secondary crosslinker, which in this case is apathogen or a product produced or induced by a pathogen); PERK; IRE1alpha; IRE1 beta; caspase 3; caspase 8 (for example, by mimicking thecaspase-8-binding DED domain from approximately amino acids 1-117 ofhuman FADD); caspase 9 (for example, by mimicking the caspase-9-bindingCARD domain from approximately amino acids 1-97 of human Apaf-1);Apaf-1; FADD (for example, by mimicking the death domain (DD) from humanFas/CD95 or TRADD); a caspase or apoptosis signaling molecule; Nod1/CARD4 (for example, by binding within the domain from approximatelyamino acids 126-953 of human Nod1/CARD4); Nod2 (for example, by bindingwithin the domain from approximately amino acids 220-1040 of humanNod2); Ipaf-1/CLAN/CARD12 (for example, by binding within the domainfrom approximately amino acids 125-1024 of human Ipaf-1/CLAN/CARD12);CIITA (for example, by binding within the nucleotide oligomerizationdomain (NOD) or leucine-rich-repeat (LRR) domain of a CIITA isoform);RIP (for example, by mimicking the death domain (DD) of Fas/CD95 orTRADD); Rip2/RICK/CARDIAK (for example, by mimicking the CARD domainfrom approximately amino acids 1-126 of human Nod1); IKK gamma (forexample, by binding with the domain from approximately amino acids201-419 of human IKK gamma); IKK alpha and/or beta (for example, bymimicking the IKK alpha/beta binding domain from approximately aminoacids 1-200 of human IKK gamma); HSF1 (for example, by binding withinthe domain from approximately amino acids 137-503 of human HSF1); aDNase as described supra; an RNase as described supra; a protease asdescribed supra; a glycosidase as described supra; a lipase as describedsupra; a heat shock protein as described supra; an E3 ubiquitin ligaseas described supra.

A chimeric molecule or agent of the invention can be a molecule thatbinds to CpG DNA (for example, by mimicking the CpG-DNA-binding domainfrom the extracellular domain of human TLR9) and that also binds to oneor more of the following: protein kinase R (for example, by bindingwithin the domain from approximately amino acids 1-174 of human proteinkinase R); RNase L (for example, by containing or by mimicking a shortmolecule of 2′,5′-oligoadenylate that binds to RNase L but does notactivate it without a secondary crosslinker, which in this case is apathogen or a product produced or induced by a pathogen); PERK; IRE1alpha; IRE1 beta; caspase 3; caspase 8 (for example, by mimicking thecaspase-8-binding DED domain from approximately amino acids 1-117 ofhuman FADD); caspase 9 (for example, by mimicking the caspase-9-bindingCARD domain from approximately amino acids 1-97 of human Apaf-1);Apaf-1; FADD (for example, by mimicking the death domain (DD) from humanFas/CD95 or TRADD); a caspase or apoptosis signaling molecule;Nod1/CARD4 (for example, by binding within the domain from approximatelyamino acids 126-953 of human Nod1/CARD4); Nod2 (for example, by bindingwithin the domain from approximately amino acids 220-1040 of humanNod2); Ipaf-1/CLAN/CARD12 (for example, by binding within the domainfrom approximately amino acids 125-1024 of human Ipaf-1/CLAN/CARD12);CIITA (for example, by binding within the nucleotide oligomerizationdomain (NOD) or leucine-rich-repeat (LRR) domain of a CIITA isoform);RIP (for example, by mimicking the death domain (DD) of Fas/CD95 orTRADD); Rip2/RICK/CARDIAK (for example, by mimicking the CARD domainfrom approximately amino acids 1-126 of human Nod1); IKK gamma (forexample, by binding with the domain from approximately amino acids201-419 of human IKK gamma); IKK alpha and/or beta (for example, bymimicking the IKK alpha/beta binding domain from approximately aminoacids 1-200 of human IKK gamma); HSF1 (for example, by binding withinthe domain from approximately amino acids 137-503 of human HSF1); aDNase as described supra; an RNase as described supra; a protease asdescribed supra; a glycosidase as described supra; a lipase as describedsupra; a heat shock protein as described supra; an E3 ubiquitin ligaseas described supra.

A chimeric molecule or agent of the invention can be a molecule thatbinds to zymosan (for example, by mimicking the zymosan-binding domainfrom the extracellular domain of human TLR2) and that also binds to oneor more of the following: protein kinase R (for example, by bindingwithin the domain from approximately amino acids 1-174 of human proteinkinase R); RNase L (for example, by containing or by mimicking a shortmolecule of 2′,5′-oligoadenylate that binds to RNase L but does notactivate it without a secondary crosslinker, which in this case is apathogen or a product produced or induced by a pathogen); PERK; IRE1alpha; IRE1 beta; caspase 3; caspase 8 (for example, by mimicking thecaspase-8-binding DED domain from approximately amino acids 1-117 ofhuman FADD); caspase 9 (for example, by mimicking the caspase-9-bindingCARD domain from approximately amino acids 1-97 of human Apaf-1);Apaf-1; FADD (for example, by mimicking the death domain (DD) from humanFas/CD95 or TRADD); a caspase or apoptosis signaling molecule;Nod1/CARD4 (for example, by binding within the domain from approximatelyamino acids 126-953 of human Nod1/CARD4); Nod2 (for example, by bindingwithin the domain from approximately amino acids 220-1040 of humanNod2); Ipaf-1/CLAN/CARD12 (for example, by binding within the domainfrom approximately amino acids 125-1024 of human Ipaf-1/CLAN/CARD12);CIITA (for example, by binding within the nucleotide oligomerizationdomain (NOD) or leucine-rich-repeat (LRR) domain of a CIITA isoform);RIP (for example, by mimicking the death domain (DD) of Fas/CD95 orTRADD); Rip2/RICK/CARDIAK (for example, by mimicking the CARD domainfrom approximately amino acids 1-126 of human Nod1); IKK gamma (forexample, by binding with the domain from approximately amino acids201-419 of human IKK gamma); IKK alpha and/or beta (for example, bymimicking the IKK alpha/beta binding domain from approximately aminoacids 1-200 of human IKK gamma); HSF1 (for example, by binding withinthe domain from approximately amino acids 137-503 of human HSF1); aDNase as described supra; an RNase as described supra; a protease asdescribed supra; a glycosidase as described supra; a lipase as describedsupra; a heat shock protein as described supra; an E3 ubiquitin ligaseas described supra.

A chimeric molecule or agent of the invention can be a molecule thatbinds to a pathogenic form of a prion (for example, by mimicking aportion of a nonpathogenic prion form (such as approximately amino acids119-136 of hamster prion protein; J. Chabry et al. (1999) Journal ofVirology 73, 6245-6250), that binds to a pathogenic prion form) and thatalso binds to one or more of the following: protein kinase R (forexample, by binding within the domain from approximately amino acids1-174 of human protein kinase R); RNase L (for example, by containing orby mimicking a short molecule of 2′,5′-oligoadenylate that binds toRNase L but does not activate it without a secondary crosslinker, whichin this case is a pathogen or a product produced or induced by apathogen); PERK; IRE1 alpha; IRE1 beta; Nod1/CARD4 (for example, bybinding within the domain from approximately amino acids 126-953 ofhuman Nod1/CARD4); Nod2 (for example, by binding within the domain fromapproximately amino acids 220-1040 of human Nod2); Ipaf-1/CLAN/CARD12(for example, by binding within the domain from approximately aminoacids 125-1024 of human Ipaf-1/CLAN/CARD12); CIITA (for example, bybinding within the nucleotide oligomerization domain (NOD) orleucine-rich-repeat (LRR) domain of a CIITA isoform); RIP (for example,by mimicking the death domain (DD) of Fas/CD95 or TRADD);Rip2/RICK/CARDIAK (for example, by mimicking the CARD domain fromapproximately amino acids 1-126 of human Nod1); IKK gamma (for example,by binding with the domain from approximately amino acids 201-419 ofhuman IKK gamma); IKK alpha and/or beta (for example, by mimicking theIKK alpha/beta binding domain from approximately amino acids 1-200 ofhuman IKK gamma); HSF1 (for example, by binding within the domain fromapproximately amino acids 137-503 of human HSF1); a DNase as describedsupra; an RNase as described supra; a protease as described supra; aprotease that is activated by crosslinking; a glycosidase as describedsupra; a lipase as described supra; a heat shock protein as describedsupra; an E3 ubiquitin ligase as described supra.

A chimeric molecule or agent of the invention can be a molecule thatbinds to Apaf-1 (for example, by mimicking the CARD domain fromapproximately amino acids 1-91 of human caspase 9) and that also bindsto one or more of the following: protein kinase R (for example, bybinding within the domain from approximately amino acids 1-174 of humanprotein kinase R); RNase L (for example, by containing or by mimicking ashort molecule of 2′,5′-oligoadenylate that binds to RNase L but doesnot activate it without a secondary crosslinker, which in this case is apathogen or a product produced or induced by a pathogen); PERK; IRE1alpha; IRE1 beta; caspase 3; caspase 8 (for example, by mimicking thecaspase-8-binding DED domain from approximately amino acids 1-117 ofhuman FADD); caspase 9 (for example, by mimicking the caspase-9-bindingCARD domain from approximately amino acids 1-97 of human Apaf-1); FADD(for example, by mimicking the death domain (DD) from human Fas/CD95 orTRADD); a caspase or apoptosis signaling molecule; Nod1/CARD4 (forexample, by binding within the domain from approximately amino acids126-953 of human Nod1/CARD4); Nod2 (for example, by binding within thedomain from approximately amino acids 220-1040 of human Nod2);Ipaf-1/CLAN/CARD12 (for example, by binding within the domain fromapproximately amino acids 125-1024 of human Ipaf-1/CLAN/CARD12); CIITA(for example, by binding within the nucleotide oligomerization domain(NOD) or leucine-rich-repeat (LRR) domain of a CIITA isoform); RIP (forexample, by mimicking the death domain (DD) of Fas/CD95 or TRADD);Rip2/RICK/CARDIAK (for example, by mimicking the CARD domain fromapproximately amino acids 1-126 of human Nod1); IKK gamma (for example,by binding with the domain from approximately amino acids 201-419 ofhuman IKK gamma); IKK alpha and/or beta (for example, by mimicking theIKK alpha/beta binding domain from approximately amino acids 1-200 ofhuman IKK gamma); HSF1 (for example, by binding within the domain fromapproximately amino acids 137-503 of human HSF1); a DNase as describedsupra; an RNase as described supra; a protease as described supra; aglycosidase as described supra; a lipase as described supra; a heatshock protein as described supra; an E3 ubiquitin ligase as describedsupra.

A chimeric molecule or agent of the invention can be a molecule thatbinds to FADD (for example, by mimicking the DED-containing domain fromapproximately amino acids 1-215 of human caspase 8) and that also bindsto one or more of the following: protein kinase R (for example, bybinding within the domain from approximately amino acids 1-174 of humanprotein kinase R); RNase L (for example, by containing or by mimicking ashort molecule of 2′,5′-oligoadenylate that binds to RNase L but doesnot activate it without a secondary crosslinker, which in this case is apathogen or a product produced or induced by a pathogen); PERK; IRE1alpha; IRE1 beta; caspase 3; caspase 8 (for example, by mimicking thecaspase-8-binding DED domain from approximately amino acids 1-117 ofhuman FADD); caspase 9 (for example, by mimicking the caspase-9-bindingCARD domain from approximately amino acids 1-97 of human Apaf-1);Apaf-1; a caspase or apoptosis signaling molecule; Nod1/CARD4 (forexample, by binding within the domain from approximately amino acids126-953 of human Nod1/CARD4); Nod2 (for example, by binding within thedomain from approximately amino acids 220-1040 of human Nod2);Ipaf-1/CLAN/CARD12 (for example, by binding within the domain fromapproximately amino acids 125-1024 of human Ipaf-1/CLAN/CARD12); CIITA(for example, by binding within the nucleotide oligomerization domain(NOD) or leucine-rich-repeat (LRR) domain of a CIITA isoform); RIP (forexample, by mimicking the death domain (DD) of Fas/CD95 or TRADD);Rip2/RICK/CARDIAK (for example, by mimicking the CARD domain fromapproximately amino acids 1-126 of human Nod1); IKK gamma (for example,by binding with the domain from approximately amino acids 201-419 ofhuman IKK gamma); IKK alpha and/or beta (for example, by mimicking theIKK alpha/beta binding domain from approximately amino acids 1-200 ofhuman IKK gamma); HSF1 (for example, by binding within the domain fromapproximately amino acids 137-503 of human HSF1); a DNase as describedsupra; an RNase as described supra; a protease as described supra; aglycosidase as described supra; a lipase as described supra; a heatshock protein as described supra; an E3 ubiquitin ligase as describedsupra.

A chimeric molecule or agent of the invention can be a molecule thatbinds to TRADD (for example, by mimicking the death domain (DD) fromapproximately amino acids 117-208 of human FADD) and that also binds toone or more of the following: protein kinase R (for example, by bindingwithin the domain from approximately amino acids 1-174 of human proteinkinase R); RNase L (for example, by containing or by mimicking a shortmolecule of 2′,5′-oligoadenylate that binds to RNase L but does notactivate it without a secondary crosslinker, which in this case is apathogen or a product produced or induced by a pathogen); PERK; IRE1alpha; IRE1 beta; caspase 3; caspase 8 (for example, by mimicking thecaspase-8-binding DED domain from approximately amino acids 1-117 ofhuman FADD); caspase 9 (for example, by mimicking the caspase-9-bindingCARD domain from approximately amino acids 1-97 of human Apaf-1);Apaf-1; a caspase or apoptosis signaling molecule; Nod1/CARD4 (forexample, by binding within the domain from approximately amino acids126-953 of human Nod1/CARD4); Nod2 (for example, by binding within thedomain from approximately amino acids 220-1040 of human Nod2);Ipaf-1/CLAN/CARD12 (for example, by binding within the domain fromapproximately amino acids 125-1024 of human Ipaf-1/CLAN/CARD12); CIITA(for example, by binding within the nucleotide oligomerization domain(NOD) or leucine-rich-repeat (LRR) domain of a CIITA isoform); RIP (forexample, by mimicking the death domain (DD) of Fas/CD95 or TRADD);Rip2/RICK/CARDIAK (for example, by mimicking the CARD domain fromapproximately amino acids 1-126 of human Nod1); IKK gamma (for example,by binding with the domain from approximately amino acids 201-419 ofhuman IKK gamma); IKK alpha and/or beta (for example, by mimicking theIKK alpha/beta binding domain from approximately amino acids 1-200 ofhuman IKK gamma); HSF1 (for example, by binding within the domain fromapproximately amino acids 137-503 of human HSF1); a DNase as describedsupra; an RNase as described supra; a protease as described supra; aglycosidase as described supra; a lipase as described supra; a heatshock protein as described supra; an E3 ubiquitin ligase as describedsupra.

A chimeric molecule or agent of the invention can be a molecule thatbinds to Fas/CD95 (for example, by mimicking the death domain (DD) fromapproximately amino acids 117-208 of human FADD) and that also binds toone or more of the following: protein kinase R (for example, by bindingwithin the domain from approximately amino acids 1-174 of human proteinkinase R); RNase L (for example, by containing or by mimicking a shortmolecule of 2′,5′-oligoadenylate that binds to RNase L but does notactivate it without a secondary crosslinker, which in this case is apathogen or a product produced or induced by a pathogen); PERK; IRE1alpha; IRE1 beta; caspase 3; caspase 8 (for example, by mimicking thecaspase-8-binding DED domain from approximately amino acids 1-117 ofhuman FADD); caspase 9 (for example, by mimicking the caspase-9-bindingCARD domain from approximately amino acids 1-97 of human Apaf-1);Apaf-1; a caspase or apoptosis signaling molecule; Nod1/CARD4 (forexample, by binding within the domain from approximately amino acids126-953 of human Nod1/CARD4); Nod2 (for example, by binding within thedomain from approximately amino acids 220-1040 of human Nod2);Ipaf-1/CLAN/CARD12 (for example, by binding within the domain fromapproximately amino acids 125-1024 of human Ipaf-1/CLAN/CARD12); CIITA(for example, by binding within the nucleotide oligomerization domain(NOD) or leucine-rich-repeat (LRR) domain of a CIITA isoform); RIP (forexample, by mimicking the death domain (DD) of Fas/CD95 or TRADD);Rip2/RICK/CARDIAK (for example, by mimicking the CARD domain fromapproximately amino acids 1-126 of human Nod1); IKK gamma (for example,by binding with the domain from approximately amino acids 201-419 ofhuman IKK gamma); IKK alpha and/or beta (for example, by mimicking theIKK alpha/beta binding domain from approximately amino acids 1-200 ofhuman IKK gamma); HSF1 (for example, by binding within the domain fromapproximately amino acids 137-503 of human HSF1); a DNase as describedsupra; an RNase as described supra; a protease as described supra; aglycosidase as described supra; a lipase as described supra; a heatshock protein as described supra; an E3 ubiquitin ligase as describedsupra.

A chimeric molecule or agent of the invention can be a molecule thatbinds to PERK (for example, by binding to the cytoplasmic domain ofPERK) and that also binds to one or more of the following: proteinkinase R (for example, by binding within the domain from approximatelyamino acids 1-174 of human protein kinase R); RNase L (for example, bycontaining or by mimicking a short molecule of 2′,5′-oligoadenylate thatbinds to RNase L but does not activate it without a secondarycrosslinker, which in this case is a pathogen or a product produced orinduced by a pathogen); caspase 3; caspase 8 (for example, by mimickingthe caspase-8-binding DED domain from approximately amino acids 1-117 ofhuman FADD); caspase 9 (for example, by mimicking the caspase-9-bindingCARD domain from approximately amino acids 1-97 of human Apaf-1);Apaf-1; FADD (for example, by mimicking the death domain (DD) from humanFas/CD95 or TRADD); a caspase or apoptosis signaling molecule;Nod1/CARD4 (for example, by binding within the domain from approximatelyamino acids 126-953 of human Nod1/CARD4); Nod2 (for example, by bindingwithin the domain from approximately amino acids 220-1040 of humanNod2); Ipaf-1/CLAN/CARD12 (for example, by binding within the domainfrom approximately amino acids 125-1024 of human Ipaf-1/CLAN/CARD12);CIITA (for example, by binding within the nucleotide oligomerizationdomain (NOD) or leucine-rich-repeat (LRR) domain of a CIITA isoform);RIP (for example, by mimicking the death domain (DD) of Fas/CD95 orTRADD); Rip2/RICK/CARDIAK (for example, by mimicking the CARD domainfrom approximately amino acids 1-126 of human Nod1); IKK gamma (forexample, by binding with the domain from approximately amino acids201-419 of human IKK gamma); IKK alpha and/or beta (for example, bymimicking the IKK alpha/beta binding domain from approximately aminoacids 1-200 of human IKK gamma); HSF1 (for example, by binding withinthe domain from approximately amino acids 137-503 of human HSF1); aDNase as described supra; an RNase as described supra; a protease asdescribed supra; a glycosidase as described supra; a lipase as describedsupra; a heat shock protein as described supra; an E3 ubiquitin ligaseas described supra.

A chimeric molecule or agent of the invention can be a molecule thatbinds to IRE1 alpha (for example, by binding to the cytoplasmic domainof IRE1 alpha) and that also binds to one or more of the following:protein kinase R (for example, by binding within the domain fromapproximately amino acids 1-174 of human protein kinase R); RNase L (forexample, by containing or by mimicking a short molecule of2′,5′-oligoadenylate that binds to RNase L but does not activate itwithout a secondary crosslinker, which in this case is a pathogen or aproduct produced or induced by a pathogen); caspase 3; caspase 8 (forexample, by mimicking the caspase-8-binding DED domain fromapproximately amino acids 1-117 of human FADD); caspase 9 (for example,by mimicking the caspase-9-binding CARD domain from approximately aminoacids 1-97 of human Apaf-1); Apaf-1; FADD (for example, by mimicking thedeath domain (DD) from human Fas/CD95 or TRADD); a caspase or apoptosissignaling molecule; Nod1/CARD4 (for example, by binding within thedomain from approximately amino acids 126-953 of human Nod1/CARD4); Nod2(for example, by binding within the domain from approximately aminoacids 220-1040 of human Nod2); Ipaf-1/CLAN/CARD12 (for example, bybinding within the domain from approximately amino acids 125-1024 ofhuman Ipaf-1/CLAN/CARD12); CIITA (for example, by binding within thenucleotide oligomerization domain (NOD) or leucine-rich-repeat (LRR)domain of a CIITA isoform); RIP (for example, by mimicking the deathdomain (DD) of Fas/CD95 or TRADD); Rip2/RICK/CARDIAK (for example, bymimicking the CARD domain from approximately amino acids 1-126 of humanNod1); IKK gamma (for example, by binding with the domain fromapproximately amino acids 201-419 of human IKK gamma); IKK alpha and/orbeta (for example, by mimicking the IKK alpha/beta binding domain fromapproximately amino acids 1-200 of human IKK gamma); HSF1 (for example,by binding within the domain from approximately amino acids 137-503 ofhuman HSF1); a DNase as described supra; an RNase as described supra; aprotease as described supra; a glycosidase as described supra; a lipaseas described supra; a heat shock protein as described supra; an E3ubiquitin ligase as described supra.

A chimeric molecule or agent of the invention can be a molecule thatbinds to IRE1 beta (for example, by binding to the cytoplasmic domain ofIRE1 beta) and that also binds to one or more of the following: proteinkinase R (for example, by binding within the domain from approximatelyamino acids 1-174 of human protein kinase R); RNase L (for example, bycontaining or by mimicking a short molecule of 2′,5′-oligoadenylate thatbinds to RNase L but does not activate it without a secondarycrosslinker, which in this case is a pathogen or a product produced orinduced by a pathogen); caspase 3; caspase 8 (for example, by mimickingthe caspase-8-binding DED domain from approximately amino acids 1-117 ofhuman FADD); caspase 9 (for example, by mimicking the caspase-9-bindingCARD domain from approximately amino acids 1-97 of human Apaf-1);Apaf-1; FADD (for example, by mimicking the death domain (DD) from humanFas/CD95 or TRADD); a caspase or apoptosis signaling molecule;Nod1/CARD4 (for example, by binding within the domain from approximatelyamino acids 126-953 of human Nod1/CARD4); Nod2 (for example, by bindingwithin the domain from approximately amino acids 220-1040 of humanNod2); Ipaf-1/CLAN/CARD12 (for example, by binding within the domainfrom approximately amino acids 125-1024 of human Ipaf-1/CLAN/CARD12);CIITA (for example, by binding within the nucleotide oligomerizationdomain (NOD) or leucine-rich-repeat (LRR) domain of a CIITA isoform);RIP (for example, by mimicking the death domain (DD) of Fas/CD95 orTRADD); Rip2/RICK/CARDIAK (for example, by mimicking the CARD domainfrom approximately amino acids 1-126 of human Nod1); IKK gamma (forexample, by binding with the domain from approximately amino acids201-419 of human IKK gamma); IKK alpha and/or beta (for example, bymimicking the IKK alpha/beta binding domain from approximately aminoacids 1-200 of human IKK gamma); HSF1 (for example, by binding withinthe domain from approximately amino acids 137-503 of human HSF1); aDNase as described supra; an RNase as described supra; a protease asdescribed supra; a glycosidase as described supra; a lipase as describedsupra; a heat shock protein as described supra; an E3 ubiquitin ligaseas described supra.

A chimeric molecule or agent of the invention can be a molecule thatbinds to Nod1/CARD4 (for example, by binding to the CARD domain fromapproximately amino acids 1-126 of human Nod1/CARD4) and that also bindsto one or more of the following: protein kinase R (for example, bybinding within the domain from approximately amino acids 1-174 of humanprotein kinase R); RNase L (for example, by containing or by mimicking ashort molecule of 2′,5′-oligoadenylate that binds to RNase L but doesnot activate it without a secondary crosslinker, which in this case is apathogen or a product produced or induced by a pathogen); PERK; IRE1alpha; IRE1 beta; caspase 3; caspase 8 (for example, by mimicking thecaspase-8-binding DED domain from approximately amino acids 1-117 ofhuman FADD); caspase 9 (for example, by mimicking the caspase-9-bindingCARD domain from approximately amino acids 1-97 of human Apaf-1);Apaf-1; FADD (for example, by mimicking the death domain (DD) from humanFas/CD95 or TRADD); a caspase or apoptosis signaling molecule; Nod2 (forexample, by binding within the domain from approximately amino acids220-1040 of human Nod2); Ipaf-1/CLAN/CARD12 (for example, by bindingwithin the domain from approximately amino acids 125-1024 of humanIpaf-1/CLAN/CARD12); CIITA (for example, by binding within thenucleotide oligomerization domain (NOD) or leucine-rich-repeat (LRR)domain of a CIITA isoform); RIP (for example, by mimicking the deathdomain (DD) of Fas/CD95 or TRADD); Rip2/RICK/CARDIAK (for example, bymimicking the CARD domain from approximately amino acids 1-126 of humanNod1); IKK gamma (for example, by binding with the domain fromapproximately amino acids 201-419 of human IKK gamma); IKK alpha and/orbeta (for example, by mimicking the IKK alpha/beta binding domain fromapproximately amino acids 1-200 of human IKK gamma); HSF1 (for example,by binding within the domain from approximately amino acids 137-503 ofhuman HSF1); a DNase as described supra; an RNase as described supra; aprotease as described supra; a glycosidase as described supra; a lipaseas described supra; a heat shock protein as described supra; an E3ubiquitin ligase as described supra.

A chimeric molecule or agent of the invention can be a molecule thatbinds to Nod2 (for example, by binding to the CARD-containing domainfrom approximately amino acids 1-220 of human Nod2) and that also bindsto one or more of the following: protein kinase R (for example, bybinding within the domain from approximately amino acids 1-174 of humanprotein kinase R); RNase L (for example, by containing or by mimicking ashort molecule of 2′,5′-oligoadenylate that binds to RNase L but doesnot activate it without a secondary crosslinker, which in this case is apathogen or a product produced or induced by a pathogen); PERK; IRE1alpha; IRE1 beta; caspase 3; caspase 8 (for example, by mimicking thecaspase-8-binding DED domain from approximately amino acids 1-117 ofhuman FADD); caspase 9 (for example, by mimicking the caspase-9-bindingCARD domain from approximately amino acids 1-97 of human Apaf-1);Apaf-1; FADD (for example, by mimicking the death domain (DD) from humanFas/CD95 or TRADD); a caspase or apoptosis signaling molecule;Nod1/CARD4 (for example, by binding within the domain from approximatelyamino acids 126-953 of human Nod1/CARD4); Ipaf-1/CLAN/CARD12 (forexample, by binding within the domain from approximately amino acids125-1024 of human Ipaf-1/CLAN/CARD12); CIITA (for example, by bindingwithin the nucleotide oligomerization domain (NOD) orleucine-rich-repeat (LRR) domain of a CIITA isoform); RIP (for example,by mimicking the death domain (DD) of Fas/CD95 or TRADD);Rip2/RICK/CARDIAK (for example, by mimicking the CARD domain fromapproximately amino acids 1-126 of human Nod1); IKK gamma (for example,by binding with the domain from approximately amino acids 201-419 ofhuman IKK gamma); IKK alpha and/or beta (for example, by mimicking theIKK alpha/beta binding domain from approximately amino acids 1-200 ofhuman IKK gamma); HSF1 (for example, by binding within the domain fromapproximately amino acids 137-503 of human HSF1); a DNase as describedsupra; an RNase as described supra; a protease as described supra; aglycosidase as described supra; a lipase as described supra; a heatshock protein as described supra; an E3 ubiquitin ligase as describedsupra.

A chimeric molecule or agent of the invention can be a molecule thatbinds to Ipaf-1/CLAN/CARD12 (for example, by binding to the CARD domainfrom approximately amino acids 1-125 of human Ipaf-1/CLAN/CARD12) andthat also binds to one or more of the following: protein kinase R (forexample, by binding within the domain from approximately amino acids1-174 of human protein kinase R); RNase L (for example, by containing orby mimicking a short molecule of 2′,5′-oligoadenylate that binds toRNase L but does not activate it without a secondary crosslinker, whichin this case is a pathogen or a product produced or induced by apathogen); PERK; IRE1 alpha; IRE1 beta; caspase 3; caspase 8 (forexample, by mimicking the caspase-8-binding DED domain fromapproximately amino acids 1-117 of human FADD); caspase 9 (for example,by mimicking the caspase-9-binding CARD domain from approximately aminoacids 1-97 of human Apaf-1); Apaf-1; FADD (for example, by mimicking thedeath domain (DD) from human Fas/CD95 or TRADD); a caspase or apoptosissignaling molecule; Nod1/CARD4 (for example, by binding within thedomain from approximately amino acids 126-953 of human Nod1/CARD4); Nod2(for example, by binding within the domain from approximately aminoacids 220-1040 of human Nod2); CIITA (for example, by binding within thenucleotide oligomerization domain (NOD) or leucine-rich-repeat (LRR)domain of a CIITA isoform); RIP (for example, by mimicking the deathdomain (DD) of Fas/CD95 or TRADD); Rip2/RICK/CARDIAK (for example, bymimicking the CARD domain from approximately amino acids 1-126 of humanNod1); IKK gamma (for example, by binding with the domain fromapproximately amino acids 201-419 of human IKK gamma); IKK alpha and/orbeta (for example, by mimicking the IKK alpha/beta binding domain fromapproximately amino acids 1-200 of human IKK gamma); HSF1 (for example,by binding within the domain from approximately amino acids 137-503 ofhuman HSF1); a DNase as described supra; an RNase as described supra; aprotease as described supra; a glycosidase as described supra; a lipaseas described supra; a heat shock protein as described supra; an E3ubiquitin ligase as described supra.

A chimeric molecule or agent of the invention can be a molecule thatbinds to CIITA (for example, by binding to the CARD and/or acidicdomains from CIITA isoforms) and that also binds to one or more of thefollowing: protein kinase R (for example, by binding within the domainfrom approximately amino acids 1-174 of human protein kinase R); RNase L(for example, by containing or by mimicking a short molecule of2′,5′-oligoadenylate that binds to RNase L but does not activate itwithout a secondary crosslinker, which in this case is a pathogen or aproduct produced or induced by a pathogen); PERK; IRE1 alpha; IRE1 beta;caspase 3; caspase 8 (for example, by mimicking the caspase-8-bindingDED domain from approximately amino acids 1-117 of human FADD); caspase9 (for example, by mimicking the caspase-9-binding CARD domain fromapproximately amino acids 1-97 of human Apaf-1); Apaf-1; FADD (forexample, by mimicking the death domain (DD) from human Fas/CD95 orTRADD); a caspase or apoptosis signaling molecule; Nod1/CARD4 (forexample, by binding within the domain from approximately amino acids126-953 of human Nod1/CARD4); Nod2 (for example, by binding within thedomain from approximately amino acids 220-1040 of human Nod2);Ipaf-1/CLAN/CARD12 (for example, by binding within the domain fromapproximately amino acids 125-1024 of human Ipaf-1/CLAN/CARD12); RIP(for example, by mimicking the death domain (DD) of Fas/CD95 or TRADD);Rip2/RICK/CARDIAK (for example, by mimicking the CARD domain fromapproximately amino acids 1-126 of human Nod1); IKK gamma (for example,by binding with the domain from approximately amino acids 201-419 ofhuman IKK gamma); IKK alpha and/or beta (for example, by mimicking theIKK alpha/beta binding domain from approximately amino acids 1-200 ofhuman IKK gamma); HSF1 (for example, by binding within the domain fromapproximately amino acids 137-503 of human HSF1); a DNase as describedsupra; an RNase as described supra; a protease as described supra; aglycosidase as described supra; a lipase as described supra; a heatshock protein as described supra; an E3 ubiquitin ligase as describedsupra.

A chimeric molecule or agent of the invention can be a molecule thatbinds to RIP (for example, by binding within the domain fromapproximately amino acids 1-289 of human RIP) and that also binds to oneor more of the following: protein kinase R (for example, by bindingwithin the domain from approximately amino acids 1-174 of human proteinkinase R); RNase L (for example, by containing or by mimicking a shortmolecule of 2′,5′-oligoadenylate that binds to RNase L but does notactivate it without a secondary crosslinker, which in this case is apathogen or a product produced or induced by a pathogen); PERK; IRE1alpha; IRE1 beta; caspase 3; caspase 8 (for example, by mimicking thecaspase-8-binding DED domain from approximately amino acids 1-117 ofhuman FADD); caspase 9 (for example, by mimicking the caspase-9-bindingCARD domain from approximately amino acids 1-97 of human Apaf-1);Apaf-1; FADD (for example, by mimicking the death domain (DD) from humanFas/CD95 or TRADD); a caspase or apoptosis signaling molecule;Nod1/CARD4 (for example, by binding within the domain from approximatelyamino acids 126-953 of human Nod1/CARD4); Nod2 (for example, by bindingwithin the domain from approximately amino acids 220-1040 of humanNod2); Ipaf-1/CLAN/CARD12 (for example, by binding within the domainfrom approximately amino acids 125-1024 of human Ipaf-1/CLAN/CARD12);CIITA (for example, by binding within the nucleotide oligomerizationdomain (NOD) or leucine-rich-repeat (LRR) domain of a CIITA isoform);Rip2/RICK/CARDIAK (for example, by mimicking the CARD domain fromapproximately amino acids 1-126 of human Nod1); IKK gamma (for example,by binding with the domain from approximately amino acids 201-419 ofhuman IKK gamma); IKK alpha and/or beta (for example, by mimicking theIKK alpha/beta binding domain from approximately amino acids 1-200 ofhuman IKK gamma); HSF1 (for example, by binding within the domain fromapproximately amino acids 137-503 of human HSF1); a DNase as describedsupra; an RNase as described supra; a protease as described supra; aglycosidase as described supra; a lipase as described supra; a heatshock protein as described supra; an E3 ubiquitin ligase as describedsupra.

A chimeric molecule or agent of the invention can be a molecule thatbinds to Rip2/RICK/CARDIAK (for example, by binding within the domainfrom approximately amino acids 1-292 of human Rip2/RICK/CARDIAK) andthat also binds to one or more of the following: protein kinase R (forexample, by binding within the domain from approximately amino acids1-174 of human protein kinase R); RNase L (for example, by containing orby mimicking a short molecule of 2′,5′-oligoadenylate that binds toRNase L but does not activate it without a secondary crosslinker, whichin this case is a pathogen or a product produced or induced by apathogen); PERK; IRE1 alpha; IRE1 beta; caspase 3; caspase 8 (forexample, by mimicking the caspase-8-binding DED domain fromapproximately amino acids 1-117 of human FADD); caspase 9 (for example,by mimicking the caspase-9-binding CARD domain from approximately aminoacids 1-97 of human Apaf-1); Apaf-1; FADD (for example, by mimicking thedeath domain (DD) from human Fas/CD95 or TRADD); a caspase or apoptosissignaling molecule; Nod1/CARD4 (for example, by binding within thedomain from approximately amino acids 126-953 of human Nod1/CARD4); Nod2(for example, by binding within the domain from approximately aminoacids 220-1040 of human Nod2); Ipaf-1/CLAN/CARD12 (for example, bybinding within the domain from approximately amino acids 125-1024 ofhuman Ipaf-1/CLAN/CARD12); CIITA (for example, by binding within thenucleotide oligomerization domain (NOD) or leucine-rich-repeat (LRR)domain of a CIITA isoform); RIP (for example, by mimicking the deathdomain (DD) of Fas/CD95 or TRADD); IKK gamma (for example, by bindingwith the domain from approximately amino acids 201-419 of human IKKgamma); IKK alpha and/or beta (for example, by mimicking the IKKalpha/beta binding domain from approximately amino acids 1-200 of humanIKK gamma); HSF1 (for example, by binding within the domain fromapproximately amino acids 137-503 of human HSF1); a DNase as describedsupra; an RNase as described supra; a protease as described supra; aglycosidase as described supra; a lipase as described supra; a heatshock protein as described supra; an E3 ubiquitin ligase as describedsupra.

A chimeric molecule or agent of the invention can be a molecule thatbinds to IKK gamma (for example, by binding within the domain fromapproximately amino acids 201-419 of human IKK gamma) and that alsobinds to one or more of the following: protein kinase R (for example, bybinding within the domain from approximately amino acids 1-174 of humanprotein kinase R); RNase L (for example, by containing or by mimicking ashort molecule of 2′,5′-oligoadenylate that binds to RNase L but doesnot activate it without a secondary crosslinker, which in this case is apathogen or a product produced or induced by a pathogen); PERK; IRE1alpha; IRE1 beta; caspase 3; caspase 8 (for example, by mimicking thecaspase-8-binding DED domain from approximately amino acids 1-117 ofhuman FADD); caspase 9 (for example, by mimicking the caspase-9-bindingCARD domain from approximately amino acids 1-97 of human Apaf-1);Apaf-1; FADD (for example, by mimicking the death domain (DD) from humanFas/CD95 or TRADD); a caspase or apoptosis signaling molecule;Nod1/CARD4 (for example, by binding within the domain from approximatelyamino acids 126-953 of human Nod1/CARD4); Nod2 (for example, by bindingwithin the domain from approximately amino acids 220-1040 of humanNod2); Ipaf-1/CLAN/CARD12 (for example, by binding within the domainfrom approximately amino acids 125-1024 of human Ipaf-1/CLAN/CARD12);CIITA (for example, by binding within the nucleotide oligomerizationdomain (NOD) or leucine-rich-repeat (LRR) domain of a CIITA isoform);RIP (for example, by mimicking the death domain (DD) of Fas/CD95 orTRADD); Rip2/RICK/CARDIAK (for example, by mimicking the CARD domainfrom approximately amino acids 1-126 of human Nod 1); HSF1 (for example,by binding within the domain from approximately amino acids 137-503 ofhuman HSF1); a DNase as described supra; an RNase as described supra; aprotease as described supra; a glycosidase as described supra; a lipaseas described supra; a heat shock protein as described supra; an E3ubiquitin ligase as described supra.

A chimeric molecule or agent of the invention can be a molecule thatbinds to HSF1 (for example, by binding within the DNA-binding domainfrom approximately amino acids 1-120 of human HSF1) and that also bindsto one or more of the following: protein kinase R (for example, bybinding within the domain from approximately amino acids 1-174 of humanprotein kinase R); RNase L (for example, by containing or by mimicking ashort molecule of 2′,5′-oligoadenylate that binds to RNase L but doesnot activate it without a secondary crosslinker, which in this case is apathogen or a product produced or induced by a pathogen); PERK; IRE1alpha; IRE1 beta; caspase 3; caspase 8 (for example, by mimicking thecaspase-8-binding DED domain from approximately amino acids 1-117 ofhuman FADD); caspase 9 (for example, by mimicking the caspase-9-bindingCARD domain from approximately amino acids 1-97 of human Apaf-1);Apaf-1; FADD (for example, by mimicking the death domain (DD) from humanFas/CD95 or TRADD); a caspase or apoptosis signaling molecule;Nod1/CARD4 (for example, by binding within the domain from approximatelyamino acids 126-953 of human Nod1/CARD4); Nod2 (for example, by bindingwithin the domain from approximately amino acids 220-1040 of humanNod2); Ipaf-1/CLAN/CARD12 (for example, by binding within the domainfrom approximately amino acids 125-1024 of human Ipaf-1/CLAN/CARD12);CIITA (for example, by binding within the nucleotide oligomerizationdomain (NOD) or leucine-rich-repeat (LRR) domain of a CIITA isoform);RIP (for example, by mimicking the death domain (DD) of Fas/CD95 orTRADD); Rip2/RICK/CARDIAK (for example, by mimicking the CARD domainfrom approximately amino acids 1-126 of human Nod1); IKK gamma (forexample, by binding with the domain from approximately amino acids201-419 of human IKK gamma); IKK alpha and/or beta (for example, bymimicking the IKK alpha/beta binding domain from approximately aminoacids 1-200 of human IKK gamma); a DNase as described supra; an RNase asdescribed supra; a protease as described supra; a glycosidase asdescribed supra; a lipase as described supra; a heat shock protein asdescribed supra; an E3 ubiquitin ligase as described supra.

A chimeric molecule or agent of the invention can be a molecule thatbinds to a pathogen or a product produced or induced by a pathogen andthat also contains an effector domain, thereby promoting ananti-pathogen effect by bringing a pathogen/pathogen-produced productinto close proximity with an anti-pathogen effector domain. Morespecifically, an agent of the invention can be a molecule (for exampleand without limitation, a single-chain antibody) that binds to apathogen or product produced or induced by a pathogen and that alsocontains one or more of the following effector domains: a DNase asdescribed supra; an RNase as described supra; a protease as describedsupra; a glycosidase as described supra; a lipase as described supra; astress response or heat shock protein as described supra; an E3ubiquitin ligase as described supra; a molecule that is toxic orinhibitory to a pathogen (including but not limited to defensins asdescribed supra or drosomycin).

A chimeric molecule or agent of the invention can be a molecule thatbinds to dsRNA (for example, by containing one or more dsRNA-bindingdomain as described supra) and that also contains one or more of thefollowing effector domains: a DNase as described supra; an RNase asdescribed supra; a protease as described supra; a glycosidase asdescribed supra; a lipase as described supra; a stress response or heatshock protein as described supra; an E3 ubiquitin ligase as describedsupra; a molecule that is toxic or inhibitory to a pathogen (includingbut not limited to defensins as described supra or drosomycin).

A chimeric molecule or agent of the invention can be a molecule thatbinds to viral late domains (for example and without restriction, bybinding to viral late domain motifs such as PTAP, PSAP, PPXY, YPDL, orYXXL, as described supra) and that also contains one or more of thefollowing effector domains: a DNase as described supra; an RNase asdescribed supra; a protease as described supra; a glycosidase asdescribed supra; a lipase as described supra; a stress response or heatshock protein as described supra; an E3 ubiquitin ligase as describedsupra; a molecule that is toxic or inhibitory to a pathogen (includingbut not limited to defensins as described supra or drosomycin).

A chimeric molecule or agent of the invention can be a molecule thatbinds to viral glycoproteins (for example and without restriction, bycontaining or mimicking the hemagglutinin-binding domain of human NKcell activation receptor NKp46) and that also contains one or more ofthe following effector domains: a DNase as described supra; an RNase asdescribed supra; a protease as described supra; a glycosidase asdescribed supra; a lipase as described supra; a stress response or heatshock protein as described supra; an E3 ubiquitin ligase as describedsupra; a molecule that is toxic or inhibitory to a pathogen (includingbut not limited to defensins as described supra or drosomycin).

A chimeric molecule or agent of the invention can be a molecule thatbinds to LPS (for example, by containing or mimicking the LPS-bindingdomain from approximately amino acids 1-199 of human BPI or otherLPS-binding domains as described supra) and that also contains one ormore of the following effector domains: a DNase as described supra; anRNase as described supra; a protease as described supra; a glycosidaseas described supra; a lipase as described supra; a stress response orheat shock protein as described supra; an E3 ubiquitin ligase asdescribed supra; a molecule that is toxic or inhibitory to a pathogen(including but not limited to defensins as described supra ordrosomycin).

A chimeric molecule or agent of the invention can be a molecule thatbinds to peptidoglycan (for example, by containing or mimicking thepeptidoglycan-binding domain from the extracellular domain of humanTLR2) and that also contains one or more of the following effectordomains: a DNase as described supra; an RNase as described supra; aprotease as described supra; a glycosidase as described supra; a lipaseas described supra; a stress response or heat shock protein as describedsupra; an E3 ubiquitin ligase as described supra; a molecule that istoxic or inhibitory to a pathogen (including but not limited todefensins as described supra or drosomycin).

A chimeric molecule or agent of the invention can be a molecule thatbinds to muramyl dipeptide (for example, by containing or mimicking themuramyl-dipeptide-binding domain from approximately amino acids 744-1040of human Nod2) and that also contains one or more of the followingeffector domains: a DNase as described supra; an RNase as describedsupra; a protease as described supra; a glycosidase as described supra;a lipase as described supra; a stress response or heat shock protein asdescribed supra; an E3 ubiquitin ligase as described supra; a moleculethat is toxic or inhibitory to a pathogen (including but not limited todefensins as described supra or drosomycin).

A chimeric molecule or agent of the invention can be a molecule thatbinds to bacterial flagellin (for example, by containing or mimickingthe flagellin-binding domain from the extracellular domain of humanTLR5) and that also contains one or more of the following effectordomains: a DNase as described supra; an RNase as described supra; aprotease as described supra; a glycosidase as described supra; a lipaseas described supra; a stress response or heat shock protein as describedsupra; an E3 ubiquitin ligase as described supra; a molecule that istoxic or inhibitory to a pathogen (including but not limited todefensins as described supra or drosomycin).

A chimeric molecule or agent of the invention can be a molecule thatbinds to a bacterial type III secretion system and that also containsone or more of the following effector domains: a DNase as describedsupra; an RNase as described supra; a protease as described supra; aglycosidase as described supra; a lipase as described supra; a stressresponse or heat shock protein as described supra; an E3 ubiquitinligase as described supra; a molecule that is toxic or inhibitory to apathogen (including but not limited to defensins as described supra ordrosomycin).

A chimeric molecule or agent of the invention can be a molecule thatbinds to CpG DNA (for example, by containing or mimicking theCpG-DNA-binding domain from the extracellular domain of human TLR9) andthat also contains one or more of the following effector domains: aDNase as described supra; an RNase as described supra; a protease asdescribed supra; a glycosidase as described supra; a lipase as describedsupra; a stress response or heat shock protein as described supra; an E3ubiquitin ligase as described supra; a molecule that is toxic orinhibitory to a pathogen (including but not limited to defensins asdescribed supra or drosomycin).

A chimeric molecule or agent of the invention can be a molecule thatbinds to zymosan (for example, by containing or mimicking thezymosan-binding domain from the extracellular domain of human TLR2) andthat also contains one or more of the following effector domains: aDNase as described supra; an RNase as described supra; a protease asdescribed supra; a glycosidase as described supra; a lipase as describedsupra; a stress response or heat shock protein as described supra; an E3ubiquitin ligase as described supra; a molecule that is toxic orinhibitory to a pathogen (including but not limited to defensins asdescribed supra or drosomycin).

A chimeric molecule or agent of the invention can be a molecule thatbinds to a pathogenic form of a prion (for example, by containing ormimicking a portion of a nonpathogenic prion form (such as approximatelyamino acids 119-136 of hamster prion protein; J. Chabry et al. (1999)Journal of Virology 73, 6245-6250) that binds to a pathogenic prionform) and that also contains one or more of the following effectordomains: a DNase as described supra; an RNase as described supra; aprotease as described supra; a glycosidase as described supra; a lipaseas described supra; a stress response or heat shock protein as describedsupra; an E3 ubiquitin ligase as described supra; a molecule that istoxic or inhibitory to a pathogen (including but not limited todefensins as described supra or drosomycin).

A chimeric molecule or agent of the invention can be a molecule thatbinds to a pathogen or a product produced or induced by a pathogen andthat also contains an effector domain, thereby promoting ananti-pathogen effect by bringing a pathogen/pathogen-produced productinto close proximity with an anti-pathogen effector domain. Morespecifically, an agent of the invention can be a molecule (for exampleand without limitation, a single-chain antibody) that binds to apathogen or product produced or induced by a pathogen and that alsocontains one or more of the following effector domains: a DNase asdescribed supra; an RNase as described supra; a protease as describedsupra; a glycosidase as described supra; a lipase as described supra; astress response or heat shock protein as described supra; an E3ubiquitin ligase as described supra; a molecule that is toxic orinhibitory to a pathogen (including but not limited to defensins asdescribed supra or drosomycin).

A chimeric molecule or agent of the invention can be a molecule thatbinds to dsRNA (for example, by containing one or more dsRNA-bindingdomain as described supra) and that also contains one or more of thefollowing effector domains: a DNase as described supra; an RNase asdescribed supra; a protease as described supra; a glycosidase asdescribed supra; a lipase as described supra; a stress response or heatshock protein as described supra; an E3 ubiquitin ligase as describedsupra; a molecule that is toxic or inhibitory to a pathogen (includingbut not limited to defensins as described supra or drosomycin).

A chimeric molecule or agent of the invention can be a molecule thatbinds to viral late domains (for example and without restriction, bybinding to viral late domain motifs such as PTAP, PSAP, PPXY, YPDL, orYXXL, as described supra) and that also contains one or more of thefollowing effector domains: a DNase as described supra; an RNase asdescribed supra; a protease as described supra; a glycosidase asdescribed supra; a lipase as described supra; a stress response or heatshock protein as described supra; an E3 ubiquitin ligase as describedsupra; a molecule that is toxic or inhibitory to a pathogen (includingbut not limited to defensins as described supra or drosomycin).

A chimeric molecule or agent of the invention can be a molecule thatbinds to viral glycoproteins (for example and without restriction, bycontaining or mimicking the hemagglutinin-binding domain of human NKcell activation receptor NKp46) and that also contains one or more ofthe following effector domains: a DNase as described supra; an RNase asdescribed supra; a protease as described supra; a glycosidase asdescribed supra; a lipase as described supra; a stress response or heatshock protein as described supra; an E3 ubiquitin ligase as describedsupra; a molecule that is toxic or inhibitory to a pathogen (includingbut not limited to defensins as described supra or drosomycin).

A chimeric molecule or agent of the invention can be a molecule thatbinds to LPS (for example, by containing or mimicking the LPS-bindingdomain from approximately amino acids 1-199 of human BPI or otherLPS-binding domains as described supra) and that also contains one ormore of the following effector domains: a DNase as described supra; anRNase as described supra; a protease as described supra; a glycosidaseas described supra; a lipase as described supra; a stress response orheat shock protein as described supra; an E3 ubiquitin ligase asdescribed supra; a molecule that is toxic or inhibitory to a pathogen(including but not limited to defensins as described supra ordrosomycin).

A chimeric molecule or agent of the invention can be a molecule thatbinds to peptidoglycan (for example, by containing or mimicking thepeptidoglycan-binding domain from the extracellular domain of humanTLR2) and that also contains one or more of the following effectordomains: a DNase as described supra; an RNase as described supra; aprotease as described supra; a glycosidase as described supra; a lipaseas described supra; a stress response or heat shock protein as describedsupra; an E3 ubiquitin ligase as described supra; a molecule that istoxic or inhibitory to a pathogen (including but not limited todefensins as described supra or drosomycin).

A chimeric molecule or agent of the invention can be a molecule thatbinds to muramyl dipeptide (for example, by containing or mimicking themuramyl-dipeptide-binding domain from approximately amino acids 744-1040of human Nod2) and that also contains one or more of the followingeffector domains: a DNase as described supra; an RNase as describedsupra; a protease as described supra; a glycosidase as described supra;a lipase as described supra; a stress response or heat shock protein asdescribed supra; an E3 ubiquitin ligase as described supra; a moleculethat is toxic or inhibitory to a pathogen (including but not limited todefensins as described supra or drosomycin).

A chimeric molecule or agent of the invention can be a molecule thatbinds to bacterial flagellin (for example, by containing or mimickingthe flagellin-binding domain from the extracellular domain of humanTLR5) and that also contains one or more of the following effectordomains: a DNase as described supra; an RNase as described supra; aprotease as described supra; a glycosidase as described supra; a lipaseas described supra; a stress response or heat shock protein as describedsupra; an E3 ubiquitin ligase as described supra; a molecule that istoxic or inhibitory to a pathogen (including but not limited todefensins as described supra or drosomycin).

A chimeric molecule or agent of the invention can be a molecule thatbinds to a bacterial type III secretion system and that also containsone or more of the following effector domains: a DNase as describedsupra; an RNase as described supra; a protease as described supra; aglycosidase as described supra; a lipase as described supra; a stressresponse or heat shock protein as described supra; an E3 ubiquitinligase as described supra; a molecule that is toxic or inhibitory to apathogen (including but not limited to defensins as described supra ordrosomycin).

A chimeric molecule or agent of the invention can be a molecule thatbinds to CpG DNA (for example, by containing or mimicking theCpG-DNA-binding domain from the extracellular domain of human TLR9) andthat also contains one or more of the following effector domains: aDNase as described supra; an RNase as described supra; a protease asdescribed supra; a glycosidase as described supra; a lipase as describedsupra; a stress response or heat shock protein as described supra; an E3ubiquitin ligase as described supra; a molecule that is toxic orinhibitory to a pathogen (including but not limited to defensins asdescribed supra or drosomycin).

A chimeric molecule or agent of the invention can be a molecule thatbinds to zymosan (for example, by containing or mimicking thezymosan-binding domain from the extracellular domain of human TLR2) andthat also contains one or more of the following effector domains: aDNase as described supra; an RNase as described supra; a protease asdescribed supra; a glycosidase as described supra; a lipase as describedsupra; a stress response or heat shock protein as described supra; an E3ubiquitin ligase as described supra; a molecule that is toxic orinhibitory to a pathogen (including but not limited to defensins asdescribed supra or drosomycin).

A chimeric molecule or agent of the invention can be a molecule thatbinds to a pathogenic form of a prion (for example, by containing ormimicking a portion of a nonpathogenic prion form (such as approximatelyamino acids 119-136 of hamster prion protein; J. Chabry et al. (1999)Journal of Virology 73, 6245-6250) that binds to a pathogenic prionform) and that also contains one or more of the following effectordomains: a DNase as described supra; an RNase as described supra; aprotease as described supra; a glycosidase as described supra; a lipaseas described supra; a stress response or heat shock protein as describedsupra; an E3 ubiquitin ligase as described supra; a molecule that istoxic or inhibitory to a pathogen (including but not limited todefensins as described supra or drosomycin).

In a preferred embodiment, the effector domain is a polynucleotidesequence that encodes for the desired effector domain, and saidpolynucleotide sequence is operatively linked with a pathogen-detectiondomain or pathogen-induced-product-detection domain that is a promoter.

A dsRNA-inducible promoter, as described supra, can be operativelylinked with a wide variety of effector domains encoded by apolynucleotide sequence, as described supra. Similarly, anapoptosis-inducible promoter, as described supra, can be operativelylinked with a wide variety of effector domains encoded by apolynucleotide sequence, as described supra. Furthermore, anunfolded-protein-response-inducible promoter orendoplasmic-reticulum-associated-protein-degradation-response-induciblepromoter, as described supra, can be operatively linked with a widevariety of effector domains encoded by a polynucleotide sequence, asdescribed supra. Examples of effector domains which areoperatively-linked to these promoters include: a chimeric molecule oragent as described herein, including but not limited to, dsRNA-activatedcaspase, 2′,5′-oligoadenylate-activated caspase, dsRNA-activated caspaseactivator, or 2′,5′-oligoadenylate-activated caspase activator; achimeric transcription factor as described herein; a molecule thatcontains two or more binding sites for a pathogen, pathogen component,or pathogen product as described herein; an antisense polynucleotide orsmall interfering RNA (G. M. Barton and R. Medzhitov (2002) Proc. Natl.Acad. Sci. USA 99, 14943-14945) that inhibits expression of a pathogengene or a host gene that aids a pathogen; a molecule that executes,stimulates, or inhibits stress or inflammatory responses, as describedsupra (including but not limited to heat shock protein 70 (Hsp70: Homosapiens, #M11717, M15432, L12723, NM_(—)016299, NM_(—)005346,NM_(—)005345, NM_(—)002155, NM_(—)021979, AF093759; Mus musculus,#XM_(—)207065, XM_(—)128584, XM_(—)128585, XM_(—)110217, NM_(—)015765,NM_(—)010481, NM_(—)008301, M76613), Hsc70 (Homo sapiens, #AF352832),Hsp90 (Homo sapiens, #M16660, NM_(—)005348, NM_(—)007355); Hsp40/Hdj-1(Homo sapiens, #X62421, NM_(—)006145, NM_(—)005880), Hsp60 (Homosapiens, #NM_(—)002156), Hsp47/CBP-2 (Homo sapiens, #D83174), Hsp100(Homo sapiens, #NM_(—)006660), Alpha-A-crystallin (Homo sapiens,#NM_(—)000394), Alpha-B-crystallin (Homo sapiens, #NM_(—)001885),Hsp27-1 (Homo sapiens, #NM_(—)001540), Hsp27-2 (Homo sapiens,#XM_(—)012054), cdc48 (S. Thoms (2002) FEBS Lett. 520, 107-110), heatshock factor 1 (HSF1: Homo sapiens, #NM_(—)005526, M64673; Mus musculus,#XM_(—)128055, X61753, Z49206; A. Mathew et al. (2001) Mol. Cell. Biol.21, 7163-7171; L. Pirkkala et al. (2001) FASEB J. 15, 1118-1131),constitutively active HSF1 as will be understood by one of skill in theart, RelA/p65 (Homo sapiens, #NM_(—)021975, Z22948, L19067; Musmusculus, #NM_(—)009045, AF199371), RelB (Homo sapiens, #NM_(—)006509;Mus musculus, #NM_(—)009046, M83380), c-Rel (Homo sapiens, #X75042,NM_(—)002908; Mus musculus, #NM_(—)009044, X15842), p50/p105/NF-kappa B1 (Homo sapiens, #NM_(—)003998, S76638, AF213884, AH009144; Musmusculus, #NM_(—)008689, AK052726, M57999), p52/p100/NF-kappa B 2 (Homosapiens, #NM_(—)002502; Mus musculus, #AF155372, AF155373,NM_(—)019408), inhibitors of kappa B (I kappa B: Homo sapiens,#AY033600, NM_(—)020529; S. Ghosh and M. Karin (2002) Cell 109,S81-S96), IKK1/I kappa B kinase alpha (IKK alpha: Homo sapiens,#AF009225, AF080157), IKK2/I kappa B kinase beta (IKK beta: Homosapiens, #AF080158; Mus musculus, #AF026524, AF088910), or NEMO/I kappaB kinase gamma (IKK gamma: Homo sapiens, #AF261086, AF091453; Musmusculus, #AF069542)); a molecule that executes, stimulates, or inhibitsunfolded protein-related or endoplasmic reticulum-associated proteindegradation-related responses, as described supra (including but notlimited to BiP/GRP78/SHPA5 (Homo sapiens, #AJ271729, AF216292, X87949,NM_(—)005347; Mus musculus, #NM_(—)022310), PKR-like endoplasmicreticulum kinase (PERK: Homo sapiens, #NP_(—)004827; Mus musculus,#AAD03337, NP_(—)034251), constitutively active PERK as will beunderstood by one of skill in the art, IRE1 alpha (Homo sapiens,#AF059198; Mus musculus, #AB031332, AF071777), constitutively activeIRE1 alpha as will be understood by one of skill in the art, IRE1 beta(Homo sapiens, #AB047079), constitutively active IRE1 beta as will beunderstood by one of skill in the art, activating transcription factor 4(ATF4: Homo sapiens, #NM_(—)001675; Mus musculus, #NM_(—)009716),activating transcription factor 6 alpha or beta (ATF6 alpha or beta:Homo sapiens, #NM_(—)007348, AF005887, AB015856; Mus musculus,#XM_(—)129579), X-box binding protein 1 (XBP1: Homo sapiens, #AB076383,AB076384; Mus musculus, #AF443192, AF027963, NM_(—)013842),CHOP-10/GADD153/DDIT3 (Homo sapiens, #NM_(—)004083; Mus musculus,#X67083, NM_(—)007837), site-1 protease (S1P: Homo sapiens,#NM_(—)003791; Mus musculus, #NM_(—)019709), site-2 protease (S2P: Homosapiens, #NM_(—)015884), presenilin-1 (Homo sapiens, #AH004968,AF416717; Mus musculus, #BC030409, NM_(—)008943, AF149111), TNFreceptor-associated factor 2 (TRAF2: Homo sapiens, #NM_(—)021138,NM_(—)145718, Mus musculus, #XM_(—)203851, XM_(—)130119, L35303), orcJUN NH2-terminal kinases (JNKs: S. Oyadomari et al. (2002) Apoptosis 7,335-345)); a single-chain antibody or other molecule that binds to apathogen, pathogen component, or cellular component that directly orindirectly aids a pathogen, as described supra; a molecule that executesor stimulates complement pathway-related responses, as described supra,including but not limited to C3 alpha, C3 beta, factor B, factor D,properdin, C1q, C1r, C1s, C4, C2, C5, C6, C7, C8, C9, factor I, factorH, C1-INH, C4 bp, S protein, clusterin, carboxypeptidase N, FHL-1,FHR-1, FHR-2, FHR-3, FHR-4, CR1, or DAF; a molecule that executes,stimulates, or inhibits toll-like-receptor-related responses,NOD-protein-related responses, (including but not limited to Nod1/CARD4(Homo sapiens, #AAD28350, AAD43922; N. Inohara et al. (1999) Journal ofBiological Chemistry 274, 14560-14567); Nod2, (Homo sapiens, #AAG33677,AAK70863, AAK70865, AAK70866, AAK70867, AAK70868; Y. Ogura et al. (2001)Journal of Biological Chemistry 276, 4812-4818; N. Inohara et al. (2003)Journal of Biological Chemistry, PMID: 12514169); Ipaf-1/CLAN/CARD12(Homo sapiens, #NM_(—)021209, AY035391; J.-L. Poyet et al. (2001)Journal of Biological Chemistry 276, 28309-28313); CIITA (Homo sapiens,#AY084054, AY084055, AF410154, NM_(—)000246, X74301; M. W. Linhoff etal. (2001) Molecular and Cellular Biology 21, 3001-3011; A.Muhlethaler-Mottet et al. (1997) EMBO Journal 16, 2851-2860); NAIP (Homosapiens, #U21912, U19251); Defcap/NAC/NALP1/CARD7 (Homo sapiens,#NM_(—)033004, NM_(—)033005, NM_(—)033006, NM_(—)033007, NM_(—)014922);NBS1/NALP2 (Homo sapiens, #AF310106, NM_(—)017852); cryopyrin/CIAS1(Homo sapiens, #AF410477, AF427617, AH011140, NM_(—)004895); RIP (Homosapiens, #U50062; S. Grimm et al. (1996) Proc. Natl. Acad. Sci. USA 93,10923-10927; H. Hsu et al. (1996) Immunity 4, 387-396);Rip2/RICK/CARDIAK (Homo sapiens, #AF064824, AF078530; N. Inohara et al.(1998) Journal of Biological Chemistry 273, 18675; M. Thome et al.(1998) Current Biology 8, 885-888); and PKK (A. Muto et al. (2002)Journal of Biological Chemistry 277, 31871-31876)), pentraxin-relatedresponses, collectin-related responses, mannose-receptor-relatedresponses, scavenger-receptor-related responses, or immune-relatedresponses, as described supra; a molecule that inhibits transportbetween the cytoplasm and the nucleus of a cell, as described supra(including but not limited to importin alpha 1 (Homo sapiens,#NM_(—)002266) with the importin beta binding domain (approximatelyamino acids 3-99) removed, importin alpha 3 (Homo sapiens,#NM_(—)002268) with the importin beta binding domain (approximatelyamino acids 3-94) removed, importin alpha 4 (Homo sapiens,#NM_(—)002267) with the importin beta binding domain (approximatelyamino acids 3-94) removed, importin alpha 5 (Homo sapiens, #U28386) withthe importin beta binding domain (approximately amino acids 3-94)removed, importin alpha 6 (Homo sapiens, #NM_(—)002269) with theimportin beta binding domain (approximately amino acids 3-94) removed,importin alpha 7 (Homo sapiens, #NM_(—)012316) with the importin betabinding domain (approximately amino acids 3-103) removed, importin alphawith the importin beta binding domain removed as described supra andalso with the last two armadillo repeats removed (Y. Miyamoto et al.(2002) EMBO Journal 21, 5833-5842) as will be understood by one of skillin the art, the autoinhibitory domain of an importin alpha mutated tohave a higher than normal affinity for wild-type importin alpha (B.Catimel et al. (2001) Journal of Biological Chemistry 276, 34189-34198)as will be understood by one of skill in the art, a modified importinalpha that does not enable nuclear import but still binds to one or morepathogen nuclear localization signals (NLSs) and does so preferably witha higher affinity than it binds to cellular NLSs as will be understoodby one of skill in the art, the importin beta binding domain of importinalpha 1 (Homo sapiens, #NM_(—)002266, approximately amino acids 1-99),the importin beta binding domain of importin alpha 3 (Homo sapiens,#NM_(—)002268, approximately amino acids 1-94), the importin betabinding domain of importin alpha 4 (Homo sapiens, #NM_(—)002267,approximately amino acids 1-94), the importin beta binding domain ofimportin alpha 5 (Homo sapiens, #U28386, approximately amino acids1-94), the importin beta binding domain of importin alpha 6 (Homosapiens, #NM_(—)002269, approximately amino acids 1-94), the importinbeta binding domain of importin alpha 7 (Homo sapiens, #NM_(—)012316,approximately amino acids 1-103), importin beta 1 (Homo sapiens,#NM_(—)002265, #NP_(—)002256) modified to not bind nucleoporins (forexample by deleting the region between HEAT-5 and HEAT-6 (approximatelyamino acids 203-211) and the region between HEAT-6 and HEAT-7(approximately amino acids 246-252) or by replacing those regions withnonhomologous linker regions (Y. M. Chook and G. Blobel (2001) CurrentOpinion in Structural Biology 11, 703-715)), importin beta 1 (Homosapiens, #NM_(—)002265, #NP_(—)002256) modified to not bind importinalpha (for example by deleting the acidic loop importin-alpha-bindingregion spanning from approximately amino acid 333 through approximatelyamino acid 343 (G. Cingolani et al. (1999) Nature 399, 221-229)), adefective mutant of an exportin (I. G. Macara (2001) Microbiology andMolecular Biology Reviews 65, 570-594) as will be understood by one ofskill in the art, a mutant p10/NTF2 that inhibits import by importinbeta 1 (for example and without limitation, p10 D23A (C. M. Lane et al.(2000) Journal of Cell Biology 151, 321-331) or N77Y (B. B. Quimby etal. (2001) Journal of Biological Chemistry 276, 38820-38829)),vesicuovirus matrix protein or a portion thereof that inhibits nuclearimport and/or nuclear export (J. M. Petersen et al. (2001) Proc. Natl.Acad. Sci. USA 98, 8590-8595; J. M. Petersen et al. (2000) Molecular andCellular Biology 20, 8590-8601; C. von Kobbe et al. (2000) MolecularCell 6, 1243-1252), a peptide that resembles the classical nuclearlocalization signal of SV40 T antigen (E. Merle et al. (1999) Journal ofCellular Biochemistry 74, 628-637), another nuclear localization signal,peptides with FxFG repeats or GLFG repeats (R. Bayliss et al. (2002)Journal of Biological Chemistry 277, 50597-50606), leptomycin B, amutant of Ran that interferes with nuclear import or export (for exampleand without limitation, RanC4A (R. H. Kehlenbach et al. (2001) Journalof Biological Chemistry 276, 14524-14531)), or a molecule that binds toa pathogen or pathogen component or cellular component that is involvedin transport between the cytoplasm and the nucleus of a cell (I. G.Macara (2001) Microbiology and Molecular Biology Reviews 65, 570-594; B.Ossareh-Nazari (2001) Traffic 2, 684-689)); a molecule that inhibitspathogenic prions (for example, approximately amino acids 119-136 ofhamster prion protein; J. Chabry et al. (1999) Journal of Virology 73,6245-6250); a molecule that alters the properties of the endocyticpathway, phagocytic pathway, endosomes, phagosomes, lysosomes, otherintracellular compartments, or vesicular trafficking to produce ananti-pathogen effect, as described supra (including but not limited todynamin-1 mutant K44A (M. Huber et al. (2001) Traffic 2, 727-736;particularly when overexpressed), cellubrevin (R. A. Fratti et al.(2002) Journal of Biological Chemistry 277, 17320-17326; particularlywhen overexpressed), Salmonella SpiC protein (NCBI Accession #U51927), adefective mutant of TassC (A. H. Lee et al. (2002) Cell. Microbiol. 4,739-750), other vesicular trafficking inhibitors, Nramp1 (P.Cuellar-Mata et al. (2002) Journal of Biological Chemistry 277,2258-2265; C. Frehel et al. (2002) Cellular Microbiology 4, 541-556; D.J. Hackam et al. (1998) J. Exp. Med. 188, 351-364; particularly whenoverexpressed), NADPH oxidase subunits or cofactors (P. V. Vignais(2002) Cell. Mol. Life Sci. 59, 1428-1459; particularly whenoverexpressed), NOS2 nitric oxide synthase (J. D. MacMicking et al.(1997) Proc. Natl. Acad. Sci. USA 94, 5243-5248; particularly whenoverexpressed), human papillomavirus 16 E5 protein (NCBI Accession#W5WLHS), bafilomycin A1, a single-chain antibody or other molecule thatbinds to vacuolar ATPase subunit a (S. B. Sato and S. Toyama (1994) J.Cell. Biol. 127, 39-53; preferably a1 or a2), antisense oligonucleotidesthat inhibit vacuolar ATPase subunits (J. E. Strasser et al. (1999)Journal of Immunology 162, 6148-6154), a peptide composed ofapproximately the 78 amino-terminal amino acids of vacuolar H+-ATPasesubunit E (M. Lu et al. (2002) Journal of Biological Chemistry 277,38409-38415), A2-cassette mutant of vacuolar H+-ATPase subunit A (N.Hernando et al. (1999) Eur. J. Biochem. 266, 293-301), a defectivemutant of subunit a1 or a2 of vacuolar H+-ATPase (S. Kawasaki-Nishi etal. (2001) Proc. Natl. Acad. Sci. USA 98, 12397-12402; S. Kawasaki-Nishiet al. (2001) 276, 47411-47420; T. Nishi and M. Forgac (2000) J. Biol.Chem. 275, 6824-6830; S. B. Peng et al. (1999) J. Biol. Chem. 274,2549-2555; T. Toyomura et al. (2000) J. Biol. Chem. 275, 8760-8765) aswill be understood by one of skill in the art, overexpression of the Cand/or H subunits of vacuolar H+-ATPase subunit E (K. K. Curtis and P.M. Kane (2002) Journal of Biological Chemistry 277, 2716-2724), otherdefective vacuolar ATPase subunit or portion of a subunit (examples ofwild-type human vacuolar ATPase subunits that can be made defective foranti-pathogen effects will be understood by one of skill in the art, andinclude, without limitation, those vacuolar ATPase subunits withAccession numbers: NM_(—)004231, NM_(—)130463, NM_(—)015994,NM_(—)001694, NM_(—)004047, NM_(—)001696, NM_(—)004691, NM_(—)001695,NM_(—)001693, NM_(—)001690, NM_(—)020632, NM_(—)004888)); a moleculethat executes, stimulates, or inhibits ubiquitin proteasome degradativepathway-related responses, as described supra (including but not limitedto CHIP (D. M. Cyr et al. (2002) Trends Biochem. Sci. 27, 368-375; J.Demand et al. (2001) Curr. Biol. 11, 1569-1577; S. Murata et al. (2001)EMBO Rep. 2, 1133-1138; particularly when overexpressed), Fbx2 (Y.Yoshida et al. (2002) Nature 418, 438-442; particularly whenoverexpressed), molecules that ubiquitinate pathogens or pathogencomponents or cellular components that assist pathogens (P. Zhou et al.(2000) Mol. Cell 6, 751-756; K. M. Sakamoto et al. (2001) Proc. Natl.Acad. Sci. USA 98, 8554-8559; N. Zheng et al. (2000) Cell 102, 533-539;D. Oyake et al. (2002) Biochemical and Biophysical ResearchCommunications 295, 370-375), or inhibitors of ubiquitination orproteasomes (J. Myung et al. (2001) Medicinal Research Reviews 21,245-273; G. Lennox et al. (1988) Neurosci. Lett. 94, 211-217; N. F.Bence et al. (2001) Science 292, 1552-1555); for example and withoutlimitation, lactacystin or epoxomicin; a molecule that executes,stimulates, or inhibits defensin-related responses, as described supra,including but not limited to alpha defensins, beta defensins, thetadefensins, plant defensins, or arthropod defensins; a molecule thatexecutes, stimulates, or inhibits cathelicidin-related responses, asdescribed supra, including but not limited to hCAP-18/LL-37, CRAMP,Bac4, OaBac5; prophenin-1, protegrin-1, or PR-39; a molecule thatexecutes, stimulates, or inhibits chemokine-related orthrombocidin-related responses, as described supra, including but notlimited to CC chemokines, CXC chemokines, C chemokines, CX3C chemokines,CC chemokine receptors, CXC chemokine receptors, C chemokine receptors,CX3C chemokine receptors, JAK proteins, STAT proteins, fibrinopeptide A,fibrinopeptide B, or thymosin beta 4; a molecule that executes,stimulates, or inhibits interferon-related or cytokine-relatedresponses, as described supra (including but not limited tointerferon-alpha (Homo sapiens, #NM_(—)002169, NM_(—)021002, J00207; Musmusculus, #NM_(—)010502, NM_(—)010503, NM_(—)010507, NM_(—)008333,M68944, M13710); interferon-beta (Homo sapiens, #M25460, NM_(—)002176;Mus musculus, #NM_(—)010510); interferon-gamma (Homo sapiens,#NM_(—)000619, J00219; Mus musculus, #M28621); interferon-delta;interferon-tau; interferon-omega (Homo sapiens, #NM_(—)002177);interleukin 1 (IL-1: Homo sapiens, #NM_(—)000575, NM_(—)012275,NM_(—)019618, NM_(—)000576, NM_(—)014439; Mus musculus, #NM_(—)019450,NM_(—)019451, AF230378); interleukin 2 (IL-2: Homo sapiens,#NM_(—)000586); interleukin 3 (IL-3: Homo sapiens, #NM_(—)000588; Musmusculus, #A02046); interleukin 4 (IL-4: Homo sapiens, #NM_(—)000589,NM_(—)172348; Mus musculus, #NM_(—)021283); interleukin 5 (IL-5: Homosapiens, #NM_(—)000879; Mus musculus, #NM_(—)010558); interleukin 6(IL-6: Homo sapiens, #NM_(—)000600; Mus musculus, #NM_(—)031168);interleukin 7 (IL-7: Homo sapiens, #NM_(—)000880, AH006906; Musmusculus, #NM_(—)008371); interleukin 9 (IL-9: Homo sapiens,#NM_(—)000590); interleukin 12 (IL-12: Homo sapiens, #NM_(—)000882,NM_(—)002187; Mus musculus, #NM_(—)008351, NM_(—)008352); interleukin 15(IL-15: Homo sapiens, #NM_(—)172174, NM_(—)172175, NM_(—)000585; Musmusculus, #NM_(—)008357); cytokine receptors and related signalingmolecules (W. E. Paul (ed.), Fundamental Immunology (4th ed.,Lippincott-Raven, Philadelphia, 1999), Chapters 21 and 22); interferontype I receptor subunit 1 (IFNAR1: Homo sapiens, #NM_(—)000629; Musmusculus, #NM_(—)010508); interferon type I receptor subunit 2 (IFNAR2:Homo sapiens, #NM_(—)000874; Mus musculus, #NM_(—)010509); janus kinase1 (JAK1: Homo sapiens, #NP_(—)002218; Mus musculus, #NP_(—)666257);janus kinase 2 (JAK2: Homo sapiens, #AAC23653, AAC23982, NP_(—)004963;Mus musculus, #NP_(—)032439, AAN62560); JAK3; Tyk2; signal transducerand activator of transcription 1 (STAT1: Homo sapiens, #NM_(—)007315,NM_(—)139266; Mus musculus, #U06924); signal transducer and activator oftranscription 2 (STAT2: Homo sapiens, #NM_(—)005419; Mus musculus,AF206162); STAT3; STAT4; STAT5; STAT6; interferon-stimulated gene factor3 gamma (ISGF3 gamma: Homo sapiens, #Q00978, NM_(—)006084; Mus musculus,#NM_(—)008394) interferon regulatory factor 1 (IRF1: Homo sapiens,#NM_(—)002198, P10914; Mus musculus, #NM_(—)008390); interferonregulatory factor 3 (IRF3: Homo sapiens, #NM_(—)001571, Z56281; Musmusculus, #NM_(—)016849, U75839, U75840); interferon regulatory factor 5(IRF5: Homo sapiens, #Q13568, U51127; Mus musculus, #AAB81997,NP_(—)036187); interferon regulatory factor 6 (IRF6: Homo sapiens,#AF027292, NM_(—)006147; Mus musculus, #U73029); interferon regulatoryfactor 7 (IRF7: Homo sapiens, #U53830, U53831, U53832, AF076494, U73036;Mus musculus, #NM_(—)016850, U73037); interferon regulatory factor 8(IRF8); a constitutively active interferon regulatory factor; proteinkinase R (PKR: Homo sapiens, #AAC50768; Mus musculus, #Q03963; S.Nanduri et al. (1998) EMBO J. 17, 5458-5465); constitutively active PKR;2′,5′-oligoadenylate synthetases (Homo sapiens forms including #P00973,P29728, AAD28543; Mus musculus forms including P11928; S. Y. Desai etal. (1995) J. Biol. Chem. 270, 3454-3461); constitutively active2′,5′-oligoadenylate synthetases; RNase L (Homo sapiens, #CAA52920);constitutively active RNase L; promyelocytic leukemia protein (PML: W.V. Bonilla et al. (2002) Journal of Virology 76, 3810-3818); p56 orrelated proteins (J. Guo et al. (2000) EMBO Journal 19, 6891-6899; G. C.Sen (2000) Seminars in Cancer Biology 10, 93-101); p200 or relatedproteins (G. C. Sen (2000) Seminars in Cancer Biology 10, 93-101); ADAR1(Homo sapiens, #U18121; Mus musculus, #NP_(—)062629); Mx1 (Homo sapiens,#NM_(—)002462); or Mx2 (Homo sapiens, #NM_(—)002463)); a molecule thatinhibits budding or release of pathogens from an infected cell, asdescribed supra (including but not limited to Hrs, particularly whenoverexpressed (N. Bishop et al. (2002) Journal of Cell Biology 157,91-101; L. Chin et al. (2001) Journal of Biological Chemistry 276,7069-7078; C. Raiborg et al. (2002) Nature Cell Biology 4, 394-398);defective Vps4 mutants such as K173Q or E228Q, particularly whenoverexpressed (J. E. Garrus et al. (2001) Cell 107, 55-65); smallinterfering RNA that inhibits Tsg101 expression (N. Bishop et al. (2002)Journal of Cell Biology 157, 91-101; J. E. Garrus et al. (2001) Cell107, 55-65); truncated AP-50 consisting of approximately amino acids121-435, or other defective mutant of AP-50, particularly whenoverexpressed (B. A. Puffer et al. (1998) Journal of Virology 72,10218-10221); WW-domain-containing fragment of LDI-1, Nedd4,Yes-associated protein, KIAA0439 gene product, or other defectiveNedd4-related proteins, particularly when overexpressed (A. Kikonyogo etal. (2001) Proc. Natl. Acad. Sci. USA 98, 11199-11204; A. Patnaik and J.W. Wills (2002) Journal of Virology 76, 2789-2795); a peptide consistingof the HIV p6 Gag PTAPP-motif-containing late (L) domain (L. VerPlank etal. (2001) Proc. Natl. Acad. Sci. USA 98, 7724-7729) or other viral late(L) domain containing PTAP, PSAP, PPXY, YPDL, or YXXL motifs (J.Martin-Serrano et al. (2001) Nature Medicine 7, 1313-1319; A. Patnaikand J. W. Wills (2002) Journal of Virology 76, 2789-2795); amino acids1-167 of Tsg101, TSG-5′ fragment of Tsg101, or similar amino-terminalfragment of Tsg101, particularly when overexpressed (D. G. Demirov etal. (2002) Proc. Natl. Acad. Sci. USA 99, 955-9601; E. L. Myers and J.F. Allen (2002) Journal of Virology 76, 11226-11235); a mutant of Tsg101(M. Babst et al. (2000) Traffic 1, 248-258; L. VerPlank et al. (2001)Proc. Natl. Acad. Sci. USA 98, 7724-7729; J. Martin-Serrano et al.(2001) Nature Medicine 7, 1313-1319; O. Pornillos et al. (2002) EMBOJournal 21, 2397-2406) with reduced capacity to aid viral budding; acasein kinase 2 (CK2) inhibitor, such as the peptide RRADDSDDDDD (SEQ IDNO: 472) (E. K. Hui and D. P. Nayak (2002) Journal of General Virology83, 3055-3066); or G protein signalling inhibitors (E. K. Hui and D. P.Nayak (2002) Journal of General Virology 83, 3055-3066); a molecule thatbinds to a cellular or pathogen molecule (for example and withoutlimitation, to one or more of the following molecules: Tsg101, Vps4,casein kinase 2, Hrs, hVps28, Eap30, Eap20, Eap45, Chmp1, Chmp2, Chmp3,Chmp4, Chmp5, Chmp6, AP-50, Nedd4-related proteins, WW-domain-containingproteins, or L-domain-containing proteins; O. Pornillos et al. (2002)TRENDS in Cell Biology 12, 569-579; P. Gomez-Puertas et al. (2000)Journal of Virology 74, 11538-11547; E. Katz et al. (2002) Journal ofVirology 76, 11637-11644) that is involved in budding or release ofpathogens from an infected cell); a molecule that executes or stimulatesapoptosis-related or other cell-death-related responses, as describedsupra (including but not limited to p53 (Homo sapiens, #AAF36354 throughAAF36382; Mus musculus, #AAC05704, AAD39535, AAF43275, AAF43276,AAK53397); Bax (Homo sapiens, #NM_(—)004324); Bid (Homo sapiens,#NM_(—)001196); apoptotic protease activating factor 1 (Apaf-1: Homosapiens, #NM_(—)013229, NM_(—)001160; Mus musculus, #NP_(—)033814);Fas/CD95 (Homo sapiens, #AAC16236, AAC16237; Mus musculus, #AAG02410);TNF receptors (Homo sapiens, #NP_(—)001056; V. Baud and M. Karin (2001)TRENDS in Cell Biology 11, 372-377; U. Sartorius et al. (2001)Chembiochem 2, 20-29); FLICE-activated death domain (FADD: Homo sapiens,#U24231; Mus musculus, #NM_(—)010175); TRADD (Homo sapiens,#NP_(—)003780, CAC38018); granzyme B (Homo sapiens, #AAH30195,NP_(—)004122; Mus musculus, #AAH02085, NP_(—)038570); constitutivelyactive granzyme B, as will be understood by one of skill in the art;Smac/DIABLO (Homo sapiens, #NM_(—)019887); caspases (including but notrestricted to Caspase 1, Homo sapiens, #NM_(—)001223; Caspase 2, Homosapiens, #NM_(—)032982, NM_(—)001224, NM_(—)032983, and NM_(—)032984;Caspase 3, Homo sapiens, #U26943; Caspase 4, Homo sapiens, #AAH17839;Caspase 5, Homo sapiens, #NP_(—)004338; Caspase 6, Homo sapiens,#NM_(—)001226 and NM_(—)032992; Caspase 7, Homo sapiens, #XM_(—)053352;Caspase 8, Homo sapiens, #NM_(—)001228; Caspase 9, Homo sapiens,#AB019197; Caspase 10, Homo sapiens, #XP_(—)027991; Caspase 13, Homosapiens, #AAC28380; Caspase 14, Homo sapiens, #NP_(—)036246; Caspase 1,Mus musculus, #BC008152; Caspase 2, Mus musculus, #NM_(—)007610; Caspase3, Mus musculus, #NM_(—)009810; Caspase 6, Mus musculus, #BC002022;Caspase 7, Mus musculus, #BC005428; Caspase 8, Mus musculus, #BC006737;Caspase 9, Mus musculus, #NM_(—)015733; Caspase 11, Mus musculus,#NM_(—)007609; Caspase 12, Mus musculus, #NM_(—)009808; Caspase 14, Musmusculus, #AF092997; and CED-3 caspase, Caenorhabditis elegans,#AF210702); a constitutively active caspase; calpains (T. Lu et al.,(2002) Biochimica et Biophysica Acta 1590, 16-26)); a molecule thatdegrades components of cells or pathogens, as described supra (forexample and without limitation: proteases, including chymotrypsin,trypsin, or elastase; DNases, including caspase-activated DNase (CAD),constitutively active CAD (N. Inohara et al. (1999) Journal ofBiological Chemistry 274, 270-274), or restriction enzymes; RNases,including RNase III (Homo sapiens, #AF189011; Escherichia coli,#NP_(—)417062, NC_(—)000913), RNt1p (Saccharomyces cerevisiae, #U27016),Pac1, (Schizosaccharomyces pombe, #X54998), RNase A, or RNase L;glycosidases, including N-glycanase, endoglycosidase H, O-glycanase,endoglycosidase F2, sialidase, or beta-galactosidase; or lipases,including phospholipase A1, phospholipase A2, phospholipase C, orphospholipase D); a molecule that is toxic to an infected host cell or apathogen cell, as described supra (including but not limited to anintracellular bacterial toxin (B. B. Finlay and P. Cossart (1997)Science 276, 718-725; C. Montecucco et al. (1994) FEBS Lett. 346, 92-98;P. O. Falnes et al. (2001) Biochemistry 40, 4349-4358) that has beenmodified so that it cannot cross cellular plasma membranes, such as theA (21 kDa) fragment of diptheria toxin; a molecule that is toxic to apathogen cell, including but not limited to penicillin, erythromycin,tetracycline, rifampin, amphotericin B, metronidazole, or mefloquine; anATP inhibitor (E. K. Hui and D. P. Nayak (2001) Virology 290, 329-341);or a toxin that inhibits transcription, translation, replication,oxidative phosphorylation, cytoskeletal processes, or other cell and/orpathogen functions).

An inflammatory response-inducible promoter, as described supra, can beoperatively linked with a wide variety of effector domains encoded by apolynucleotide sequence, as described supra. Similarly, a stress/heatshock-inducible promoter, as described supra, can be operatively linkedwith a wide variety of effector domains encoded by a polynucleotidesequence, as described supra. Likewise, a promoter that can be inducedby cytokines such as interferon alpha, interferon beta, or interferonomega, as described supra, can be operatively linked with a wide varietyof effector domains encoded by a polynucleotide sequence, as describedsupra. Additionally, a promoter that can be induced by cytokines such asinterferon gamma, interleukin 1, interleukin 2, interleukin 3,interleukin 4, interleukin 5, interleukin 6, interleukin 7, interleukin9, interleukin 12, or interleukin 15, as described supra, can beoperatively linked with a wide variety of effector domains encoded by apolynucleotide sequence, as described supra. Alternatively, adrug-inducible promoter, as described supra, can be operatively linkedwith a wide variety of effector domains encoded by a polynucleotidesequence, as described supra. Examples of the effector domains that canbe operatively linked to these promoters, include: a chimeric moleculeor agent as described herein, including but not limited to,dsRNA-activated caspase, 2′,5′-oligoadenylate-activated caspase,dsRNA-activated caspase activator, or 2′,5′-oligoadenylate-activatedcaspase activator; a chimeric transcription factor as described herein;a molecule that contains two or more binding sites for a pathogen,pathogen component, or pathogen product as described herein; anantisense polynucleotide or small interfering RNA (G. M. Barton and R.Medzhitov (2002) Proc. Natl. Acad. Sci. USA 99, 14943-14945) thatinhibits expression of a pathogen gene or a host gene that aids apathogen; a molecule that executes, stimulates, or inhibits stress orinflammatory responses, as described supra (including but not limited toheat shock protein 70 (Hsp70: Homo sapiens, #M11717, M15432, L12723,NM_(—)016299, NM_(—)005346, NM_(—)005345, NM_(—)002155, NM_(—)021979,AF093759; Mus musculus, #XM_(—)207065, XM_(—)128584, XM_(—)128585,XM_(—)110217, NM_(—)015765, NM_(—)010481, NM_(—)008301, M76613), Hsc70(Homo sapiens, #AF352832), Hsp90 (Homo sapiens, #M16660, NM_(—)005348,NM_(—)007355); Hsp40/Hdj-1 (Homo sapiens, #X62421, NM_(—)006145,NM_(—)005880), Hsp60 (Homo sapiens, #NM_(—)002156), Hsp47/CBP-2 (Homosapiens, #D83174), Hsp100 (Homo sapiens, #NM_(—)006660),Alpha-A-crystallin (Homo sapiens, #NM_(—)000394), Alpha-B-crystallin(Homo sapiens, #NM_(—)001885), Hsp27-1 (Homo sapiens, #NM_(—)001540),Hsp27-2 (Homo sapiens, #XM_(—)012054), cdc48 (S. Thoms (2002) FEBS Lett.520, 107-110), heat shock factor 1 (HSF1: Homo sapiens, #NM_(—)005526,M64673; Mus musculus, #XM_(—)128055, X61753, Z49206; A. Mathew et al.(2001) Mol. Cell. Biol. 21, 7163-7171; L. Pirkkala et al. (2001) FASEBJ. 15, 1118-1131), constitutively active HSF1, RelA/p65 (Homo sapiens,#NM_(—)021975, Z22948, L19067; Mus musculus, #NM_(—)009045, AF199371),RelB (Homo sapiens, #NM_(—)006509; Mus musculus, #NM_(—)009046, M83380),c-Rel (Homo sapiens, #X75042, NM_(—)002908; Mus musculus, #NM_(—)009044,X15842), p50/p105/NF-kappa B 1 (Homo sapiens, #NM_(—)003998, S76638,AF213884, AH009144; Mus musculus, #NM_(—)008689, AK052726, M57999),p52/p100/NF-kappa B 2 (Homo sapiens, #NM_(—)002502; Mus musculus,#AF155372, AF155373, NM_(—)019408), inhibitors of kappa B (I kappa B:Homo sapiens, #AY033600, NM_(—)020529; S. Ghosh and M. Karin (2002) Cell109, S81-S96), IKK1/I kappa B kinase alpha (IKK alpha: Homo sapiens,#AF009225, AF080157), IKK2/I kappa B kinase beta (IKK beta: Homosapiens, #AF080158; Mus musculus, #AF026524, AF088910), or NEMO/I kappaB kinase gamma (IKK gamma: Homo sapiens, #AF261086, AF091453; Musmusculus, #AF069542)); a molecule that executes, stimulates, or inhibitsunfolded-protein-related or endoplasmic reticulum-associated proteindegradation-related responses, as described supra (including but notlimited to BiP/GRP78/SHPA5 (Homo sapiens, #AJ271729, AF216292, X87949,NM_(—)005347; Mus musculus, #NM_(—)022310), PKR-like endoplasmicreticulum kinase (PERK: Homo sapiens, #NP_(—)004827; Mus musculus,#AAD03337, NP_(—)034251), constitutively active PERK, IRE1 alpha (Homosapiens, #AF059198; Mus musculus, #AB031332, AF071777), constitutivelyactive IRE1 alpha as will be understood by one of skill in the art, IRE1beta (Homo sapiens, #AB047079), constitutively active IRE1 beta,activating transcription factor 4 (ATF4: Homo sapiens, #NM_(—)001675;Mus musculus, #NM_(—)009716), activating transcription factor 6 alpha orbeta (ATF6 alpha or beta: Homo sapiens, #NM_(—)007348, AF005887,AB015856; Mus musculus, #XM_(—)129579), X-box binding protein 1 (XBP1:Homo sapiens, #AB076383, AB076384; Mus musculus, #AF443192, AF027963,NM_(—)013842), CHOP-10/GADD153/DDIT3 (Homo sapiens, #NM_(—)004083; Musmusculus, #X67083, NM_(—)007837), site-1 protease (S1P: Homo sapiens,#NM_(—)003791; Mus musculus, #NM_(—)019709), site-2 protease (S2P: Homosapiens, #NM_(—)015884), presenilin-1 (Homo sapiens, #AH004968,AF416717; Mus musculus, #BC030409, NM_(—)008943, AF149111), TNFreceptor-associated factor 2 (TRAF2: Homo sapiens, #NM_(—)021138,NM_(—)145718, Mus musculus, #XM_(—)203851, XM_(—)130119, L35303), orcJUN NH2-terminal kinases (JNKs: S. Oyadomari et al. (2002) Apoptosis 7,335-345)); a single-chain antibody or other molecule that binds to apathogen, pathogen component, or cellular component that directly orindirectly aids a pathogen, as described supra; a molecule that executesor stimulates complement pathway-related responses, as described supra,including but not limited to C3 alpha, C3 beta, factor B, factor D,properdin, C1q, C1r, C1s, C4, C2, C5, C6, C7, C8, C9, factor I, factorH, C1-INH, C4 bp, S protein, clusterin, carboxypeptidase N, FHL-1,FHR-1, FHR-2, FHR-3, FHR-4, CR1, or DAF; a molecule that executes,stimulates, or inhibits toll-like-receptor-related responses,NOD-protein-related responses, (including but not limited to Nod1/CARD4(Homo sapiens, #AAD28350, AAD43922; N. Inohara et al. (1999) Journal ofBiological Chemistry 274, 14560-14567); Nod2, (Homo sapiens, #AAG33677,AAK70863, AAK70865, AAK70866, AAK70867, AAK70868; Y. Ogura et al. (2001)Journal of Biological Chemistry 276, 4812-4818; N. Inohara et al. (2003)Journal of Biological Chemistry, PMID: 12514169); Ipaf-1/CLAN/CARD12(Homo sapiens, #NM_(—)021209, AY035391; J.-L. Poyet et al. (2001)Journal of Biological Chemistry 276, 28309-28313); CIITA (Homo sapiens,#AY084054, AY084055, AF410154, NM_(—)000246, X74301; M. W. Linhoff etal. (2001) Molecular and Cellular Biology 21, 3001-3011; A.Muhlethaler-Mottet et al. (1997) EMBO Journal 16, 2851-2860); NAIP (Homosapiens, #U21912, U19251); Defcap/NAC/NALP1/CARD7 (Homo sapiens,#NM_(—)033004, NM_(—)033005, NM_(—)033006, NM_(—)033007, NM_(—)014922);NBS1/NALP2 (Homo sapiens, #AF310106, NM_(—)017852); cryopyrin/CIAS1(Homo sapiens, #AF410477, AF427617, AH011140, NM_(—)004895); RIP (Homosapiens, #U50062; S. Grimm et al. (1996) Proc. Natl. Acad. Sci. USA 93,10923-10927; H. Hsu et al. (1996) Immunity 4, 387-396);Rip2/RICK/CARDIAK (Homo sapiens, #AF064824, AF078530; N. Inohara et al.(1998) Journal of Biological Chemistry 273, 18675; M. Thome et al.(1998) Current Biology 8, 885-888); and PKK (A. Muto et al. (2002)Journal of Biological Chemistry 277, 31871-31876)), pentraxin-relatedresponses, collectin-related responses, mannose-receptor-relatedresponses, scavenger receptor-related responses, or immune-relatedresponses, as described supra; a molecule that inhibits transportbetween the cytoplasm and the nucleus of a cell, as described supra(including but not limited to importin alpha 1 (Homo sapiens,#NM_(—)002266) with the importin beta binding domain (approximatelyamino acids 3-99) removed, importin alpha 3 (Homo sapiens,#NM_(—)002268) with the importin beta binding domain (approximatelyamino acids 3-94) removed, importin alpha 4 (Homo sapiens,#NM_(—)002267) with the importin beta binding domain (approximatelyamino acids 3-94) removed, importin alpha 5 (Homo sapiens, #U28386) withthe importin beta binding domain (approximately amino acids 3-94)removed, importin alpha 6 (Homo sapiens, #NM_(—)002269) with theimportin beta binding domain (approximately amino acids 3-94) removed,importin alpha 7 (Homo sapiens, #NM_(—)012316) with the importin betabinding domain (approximately amino acids 3-103) removed, importin alphawith the importin beta binding domain removed as described supra andalso with the last two armadillo repeats removed (Y. Miyamoto et al.(2002) EMBO Journal 21, 5833-5842), the autoinhibitory domain of animportin alpha mutated to have a higher than normal affinity forwild-type importin alpha (B. Catimel et al. (2001) Journal of BiologicalChemistry 276, 34189-34198), a modified importin alpha that does notenable nuclear import but still binds to one or more pathogen nuclearlocalization signals (NLSs) and does so preferably with a higheraffinity than it binds to cellular NLSs, the importin beta bindingdomain of importin alpha 1 (Homo sapiens, #NM_(—)002266, approximatelyamino acids 1-99), the importin beta binding domain of importin alpha 3(Homo sapiens, #NM_(—)002268, approximately amino acids 1-94), theimportin beta binding domain of importin alpha 4 (Homo sapiens,#NM_(—)002267, approximately amino acids 1-94), the importin betabinding domain of importin alpha 5 (Homo sapiens, #U28386, approximatelyamino acids 1-94), the importin beta binding domain of importin alpha 6(Homo sapiens, #NM_(—)002269, approximately amino acids 1-94), theimportin beta binding domain of importin alpha 7 (Homo sapiens,#NM_(—)012316, approximately amino acids 1-103), importin beta 1 (Homosapiens, #NM_(—)002265, #NP_(—)002256) modified to not bind nucleoporins(for example and without limitation, by deleting the region betweenHEAT-5 and HEAT-6 (approximately amino acids 203-211) and the regionbetween HEAT-6 and HEAT-7 (approximately amino acids 246-252) or byreplacing those regions with nonhomologous linker regions (Y. M. Chookand G. Blobel (2001) Current Opinion in Structural Biology 11,703-715)), importin beta 1 (Homo sapiens, #NM_(—)002265, #NP_(—)002256)modified to not bind importin alpha (for example and without limitation,by deleting the acidic loop importin-alpha-binding region spanning fromapproximately amino acid 333 through approximately amino acid 343 (G.Cingolani et al. (1999) Nature 399, 221-229)), a defective mutant of anexportin (I. G. Macara (2001) Microbiology and Molecular Biology Reviews65, 570-594), a mutant p10/NTF2 that inhibits import by importin beta 1(for example and without limitation, p10 D23A (C. M. Lane et al. (2000)Journal of Cell Biology 151, 321-331) or N77Y (B. B. Quimby et al.(2001) Journal of Biological Chemistry 276, 38820-38829)), vesicuovirusmatrix protein or a portion thereof that inhibits nuclear import and/ornuclear export (J. M. Petersen et al. (2001) Proc. Natl. Acad. Sci. USA98, 8590-8595; J. M. Petersen et al. (2000) Molecular and CellularBiology 20, 8590-8601; C. von Kobbe et al. (2000) Molecular Cell 6,1243-1252), a peptide that resembles the classical nuclear localizationsignal of SV40 T antigen (E. Merle et al. (1999) Journal of CellularBiochemistry 74, 628-637), another nuclear localization signal, peptideswith FxFG repeats or GLFG repeats (R. Bayliss et al. (2002) Journal ofBiological Chemistry 277, 50597-50606), leptomycin B, a mutant of Ranthat interferes with nuclear import or export (for example and withoutlimitation, RanC4A (R. H. Kehlenbach et al. (2001) Journal of BiologicalChemistry 276, 14524-14531)), or a molecule that binds to a pathogen orpathogen component or cellular component that is involved in transportbetween the cytoplasm and the nucleus of a cell (I. G. Macara (2001)Microbiology and Molecular Biology Reviews 65, 570-594; B.Ossareh-Nazari (2001) Traffic 2, 684-689)); a molecule that inhibitspathogenic prions (for example and without restriction, approximatelyamino acids 119-136 of hamster prion protein; J. Chabry et al. (1999)Journal of Virology 73, 6245-6250); a molecule that alters theproperties of the endocytic pathway, phagocytic pathway, endosomes,phagosomes, lysosomes, other intracellular compartments, or vesiculartrafficking to produce an anti-pathogen effect, as described supra(including but not limited to dynamin-1 mutant K44A (M. Huber et al.(2001) Traffic 2, 727-736; particularly when overexpressed), cellubrevin(R. A. Fratti et al. (2002) Journal of Biological Chemistry 277,17320-17326; particularly when overexpressed), Salmonella SpiC protein(NCBI Accession #U51927), a defective mutant of TassC (A. H. Lee et al.(2002) Cell. Microbiol. 4, 739-750), other vesicular traffickinginhibitors, Nramp1 (P. Cuellar-Mata et al. (2002) Journal of BiologicalChemistry 277, 2258-2265; C. Frehel et al. (2002) Cellular Microbiology4, 541-556; D. J. Hackam et al. (1998) J. Exp. Med. 188, 351-364;particularly when overexpressed), NADPH oxidase subunits or cofactors(P. V. Vignais (2002) Cell. Mol. Life Sci. 59, 1428-1459; particularlywhen overexpressed), NOS2 nitric oxide synthase (J. D. MacMicking et al.(1997) Proc. Natl. Acad. Sci. USA 94, 5243-5248; particularly whenoverexpressed), human papillomavirus 16 E5 protein (NCBI Accession#W5WLHS), bafilomycin A1, a single-chain antibody or other molecule thatbinds to vacuolar ATPase subunit a (S. B. Sato and S. Toyama (1994) J.Cell. Biol. 127, 39-53; preferably a1 or a2), antisense oligonucleotidesthat inhibit vacuolar ATPase subunits (J. E. Strasser et al. (1999)Journal of Immunology 162, 6148-6154), a peptide composed ofapproximately the 78 amino-terminal amino acids of vacuolar H+-ATPasesubunit E (M. Lu et al. (2002) Journal of Biological Chemistry 277,38409-38415), A2-cassette mutant of vacuolar H+-ATPase subunit A (N.Hernando et al. (1999) Eur. J. Biochem. 266, 293-301), a defectivemutant of subunit a1 or a2 of vacuolar H+-ATPase (S. Kawasaki-Nishi etal. (2001) Proc. Natl. Acad. Sci. USA 98, 12397-12402; S. Kawasaki-Nishiet al. (2001) 276, 47411-47420; T. Nishi and M. Forgac (2000) J. Biol.Chem. 275, 6824-6830; S. B. Peng et al. (1999) J. Biol. Chem. 274,2549-2555; T. Toyomura et al. (2000) J. Biol. Chem. 275, 8760-8765),overexpression of the C and/or H subunits of vacuolar H+-ATPase subunitE (K. K. Curtis and P. M. Kane (2002) Journal of Biological Chemistry277, 2716-2724), other defective vacuolar ATPase subunit or portion of asubunit (examples of wild-type human vacuolar ATPase subunits that canbe made defective for anti-pathogen effects will be understood by one ofskill in the art, and include, without limitation, those vacuolar ATPasesubunits with Accession numbers: NM_(—)004231, NM_(—)130463,NM_(—)015994, NM_(—)001694, NM_(—)004047, NM_(—)001696, NM_(—)004691,NM_(—)001695, NM_(—)001693, NM_(—)001690, NM_(—)020632, NM_(—)004888));a molecule that executes, stimulates, or inhibits ubiquitin proteasomedegradative pathway-related responses, as described supra (including butnot limited to CHIP (D. M. Cyr et al. (2002) Trends Biochem. Sci. 27,368-375; J. Demand et al. (2001) Curr. Biol. 11, 1569-1577; S. Murata etal. (2001) EMBO Rep. 2, 1133-1138; particularly when overexpressed aswill be understood by one of skill in the art), Fbx2 (Y. Yoshida et al.(2002) Nature 418, 438-442; particularly when overexpressed), moleculesthat ubiquitinate pathogens or pathogen components or cellularcomponents that assist pathogens (P. Zhou et al. (2000) Mol. Cell 6,751-756; K. M. Sakamoto et al. (2001) Proc. Natl. Acad. Sci. USA 98,8554-8559; N. Zheng et al. (2000) Cell 102, 533-539; D. Oyake et al.(2002) Biochemical and Biophysical Research Communications 295,370-375), or inhibitors of ubiquitination or proteasomes (J. Myung etal. (2001) Medicinal Research Reviews 21, 245-273; G. Lennox et al.(1988) Neurosci. Lett. 94, 211-217; N. F. Bence et al. (2001) Science292, 1552-1555; for example and without limitation, lactacystin orepoxomicin)); a molecule that executes, stimulates, or inhibitsdefensin-related responses, as described supra, including but notlimited to alpha defensins, beta defensins, theta defensins, plantdefensins, or arthropod defensins; a molecule that executes, stimulates,or inhibits cathelicidin-related responses, as described supra,including but not limited to hCAP-18/LL-37, CRAMP, Bac4, OaBac5;prophenin-1, protegrin-1, or PR-39; a molecule that executes,stimulates, or inhibits chemokine-related or thrombocidin-relatedresponses, as described supra, including but not limited to CCchemokines, CXC chemokines, C chemokines, CX3C chemokines, CC chemokinereceptors, CXC chemokine receptors, C chemokine receptors, CX3Cchemokine receptors, JAK proteins, STAT proteins, fibrinopeptide A,fibrinopeptide B, or thymosin beta 4; a molecule that executes,stimulates, or inhibits interferon-related or cytokine-relatedresponses, as described supra (including but not limited tointerferon-alpha (Homo sapiens, #NM_(—)002169, NM_(—)021002, J00207; Musmusculus, #NM_(—)010502, NM_(—)010503, NM_(—)010507, NM_(—)008333,M68944, M13710); interferon-beta (Homo sapiens, #M25460, NM_(—)002176;Mus musculus, #NM_(—)010510); interferon-gamma (Homo sapiens,#NM_(—)000619, J00219; Mus musculus, #M28621); interferon-delta;interferon-tau; interferon-omega (Homo sapiens, #NM_(—)002177);interleukin 1 (IL-1: Homo sapiens, #NM_(—)000575, NM_(—)012275,NM_(—)019618, NM_(—)000576, NM_(—)014439; Mus musculus, #NM_(—)019450,NM_(—)019451, AF230378); interleukin 2 (IL-2: Homo sapiens,#NM_(—)000586); interleukin 3 (IL-3: Homo sapiens, #NM_(—)000588; Musmusculus, #A02046); interleukin 4 (IL-4: Homo sapiens, #NM_(—)000589,NM_(—)172348; Mus musculus, #NM_(—)021283); interleukin 5 (IL-5: Homosapiens, #NM_(—)000879; Mus musculus, #NM_(—)010558); interleukin 6(IL-6: Homo sapiens, #NM_(—)000600; Mus musculus, #NM_(—)031168);interleukin 7 (IL-7: Homo sapiens, #NM_(—)000880, AH006906; Musmusculus, #NM_(—)008371); interleukin 9 (IL-9: Homo sapiens,#NM_(—)000590); interleukin 12 (IL-12: Homo sapiens, #NM_(—)000882,NM_(—)002187; Mus musculus, #NM_(—)008351, NM_(—)008352); interleukin 15(IL-15: Homo sapiens, #NM_(—)172174, NM_(—)172175, NM_(—)000585; Musmusculus, #NM_(—)008357); cytokine receptors and related signalingmolecules (W. E. Paul (ed.), Fundamental Immunology (4th ed.,Lippincott-Raven, Philadelphia, 1999), Chapters 21 and 22); interferontype I receptor subunit 1 (IFNAR1: Homo sapiens, #NM_(—)000629; Musmusculus, #NM_(—)010508); interferon type I receptor subunit 2 (IFNAR2:Homo sapiens, #NM_(—)000874; Mus musculus, #NM_(—)010509); janus kinase1 (JAK1: Homo sapiens, #NP_(—)002218; Mus musculus, #NP_(—)666257);janus kinase 2 (JAK2: Homo sapiens, #AAC23653, AAC23982, NP_(—)004963;Mus musculus, #NP_(—)032439, AAN62560); JAK3; Tyk2; signal transducerand activator of transcription 1 (STAT1: Homo sapiens, #NM_(—)007315,NM_(—)139266; Mus musculus, #U06924); signal transducer and activator oftranscription 2 (STAT2: Homo sapiens, #NM_(—)005419; Mus musculus,AF206162); STAT3; STAT4; STAT5; STAT6; interferon-stimulated gene factor3 gamma (ISGF3 gamma: Homo sapiens, #Q00978, NM_(—)006084; Mus musculus,#NM_(—)008394) interferon regulatory factor 1 (IRF1: Homo sapiens,#NM_(—)002198, P10914; Mus musculus, #NM_(—)008390); interferonregulatory factor 3 (IRF3: Homo sapiens, #NM_(—)001571, Z56281; Musmusculus, #NM_(—)016849, U75839, U75840); interferon regulatory factor 5(IRF5: Homo sapiens, #Q13568, U51127; Mus musculus, #AAB81997,NP_(—)036187); interferon regulatory factor 6 (IRF6: Homo sapiens,#AF027292, NM_(—)006147; Mus musculus, #U73029); interferon regulatoryfactor 7 (IRF7: Homo sapiens, #U53830, U53831, U53832, AF076494, U73036;Mus musculus, #NM_(—)016850, U73037); interferon regulatory factor 8(IRF8); a constitutively active interferon regulatory factor, as will beunderstood by one of skill in the art; protein kinase R (PKR: Homosapiens, #AAC50768; Mus musculus, #Q03963; S. Nanduri et al. (1998) EMBOJ. 17, 5458-5465); 2′,5′-oligoadenylate synthetases (Homo sapiens formsincluding #P00973, P29728, AAD28543; Mus musculus forms includingP11928; S. Y. Desai et al. (1995) J. Biol. Chem. 270, 3454-3461); RNaseL (Homo sapiens, #CAA52920); promyelocytic leukemia protein (PML: W. V.Bonilla et al. (2002) Journal of Virology 76, 3810-3818); p56 or relatedproteins (J. Guo et al. (2000) EMBO Journal 19, 6891-6899; G. C. Sen(2000) Seminars in Cancer Biology 10, 93-101); p200 or related proteins(G. C. Sen (2000) Seminars in Cancer Biology 10, 93-101); ADAR1 (Homosapiens, #U18121; Mus musculus, #NP_(—)062629); Mx1 (Homo sapiens,#NM_(—)002462); or Mx2 (Homo sapiens, #NM_(—)002463)); a molecule thatinhibits budding or release of pathogens from an infected cell, asdescribed supra (including but not limited to Hrs, particularly whenoverexpressed (N. Bishop et al. (2002) Journal of Cell Biology 157,91-101; L. Chin et al. (2001) Journal of Biological Chemistry 276,7069-7078; C. Raiborg et al. (2002) Nature Cell Biology 4, 394-398);defective Vps4 mutants such as K173Q or E228Q, particularly whenoverexpressed (J. E. Garrus et al. (2001) Cell 107, 55-65); smallinterfering RNA that inhibits Tsg101 expression (N. Bishop et al. (2002)Journal of Cell Biology 157, 91-101; J. E. Garrus et al. (2001) Cell107, 55-65); truncated AP-50 consisting of approximately amino acids121-435, or other defective mutant of AP-50, particularly whenoverexpressed (B. A. Puffer et al. (1998) Journal of Virology 72,10218-10221); WW-domain-containing fragment of LDI-1, Nedd4,Yes-associated protein, KIAA0439 gene product, or other defectiveNedd4-related proteins, particularly when overexpressed (A. Kikonyogo etal. (2001) Proc. Natl. Acad. Sci. USA 98, 11199-11204; A. Patnaik and J.W. Wills (2002) Journal of Virology 76, 2789-2795); a peptide consistingof the HIV p6 Gag PTAPP-motif-containing late (L) domain (L. VerPlank etal. (2001) Proc. Natl. Acad. Sci. USA 98, 7724-7729) or other viral late(L) domain containing PTAP, PSAP, PPXY, YPDL, or YXXL motifs (J.Martin-Serrano et al. (2001) Nature Medicine 7, 1313-1319; A. Patnaikand J. W. Wills (2002) Journal of Virology 76, 2789-2795); amino acids1-167 of Tsg101, TSG-5′ fragment of Tsg101, or similar amino-terminalfragment of Tsg101, particularly when overexpressed (D. G. Demirov etal. (2002) Proc. Natl. Acad. Sci. USA 99, 955-9601; E. L. Myers and J.F. Allen (2002) Journal of Virology 76, 11226-11235); a mutant of Tsg101(M. Babst et al. (2000) Traffic 1, 248-258; L. VerPlank et al. (2001)Proc. Natl. Acad. Sci. USA 98, 7724-7729; J. Martin-Serrano et al.(2001) Nature Medicine 7, 1313-1319; O. Pornillos et al. (2002) EMBOJournal 21, 2397-2406) with reduced capacity to aid viral budding, aswill be understood by one of skill in the art; a casein kinase 2 (CK2)inhibitor, such as the peptide RRADDSDDDDD (SEQ ID NO: 472)(E. K. Huiand D. P. Nayak (2002) Journal of General Virology 83, 3055-3066); or Gprotein signalling inhibitors (E. K. Hui and D. P. Nayak (2002) Journalof General Virology 83, 3055-3066); a molecule that binds to a cellularor pathogen molecule (for example and without limitation, to one or moreof the following molecules: Tsg101, Vps4, casein kinase 2, Hrs, hVps28,Eap30, Eap20, Eap45, Chmp1, Chmp2, Chmp3, Chmp4, Chmp5, Chmp6, AP-50,Nedd4-related proteins, WW-domain-containing proteins, orL-domain-containing proteins; O. Pornillos et al. (2002) TRENDS in CellBiology 12, 569-579; P. Gomez-Puertas et al. (2000) Journal of Virology74, 11538-11547; E. Katz et al. (2002) Journal of Virology 76,11637-11644) that is involved in budding or release of pathogens from aninfected cell); a molecule that makes a cell more receptive to apoptosissignals, as described supra (including but not limited to p53 (Homosapiens, #AAF36354 through AAF36382; Mus musculus, #AAC05704, AAD39535,AAF43275, AAF43276, AAK53397); Bax (Homo sapiens, #NM_(—)004324); Bid(Homo sapiens, #NM_(—)001196); apoptotic protease activating factor 1(Apaf-1: Homo sapiens, #NM_(—)013229, NM_(—)001160; Mus musculus,#NP_(—)033814); Fas/CD95 (Homo sapiens, #AAC16236, AAC16237; Musmusculus, #AAG02410); TNF receptors (Homo sapiens, #NP_(—)001056; V.Baud and M. Karin (2001) TRENDS in Cell Biology 11, 372-377; U.Sartorius et al. (2001) Chembiochem 2, 20-29); FLICE-activated deathdomain (FADD: Homo sapiens, #U24231; Mus musculus, #NM_(—)010175); TRADD(Homo sapiens, #NP_(—)003780, CAC38018); Smac/DIABLO (Homo sapiens,#NM_(—)019887); caspases (including but not restricted to Caspase 1,Homo sapiens, #NM_(—)001223; Caspase 2, Homo sapiens, #NM_(—)032982,NM_(—)001224, NM_(—)032983, and NM_(—)032984; Caspase 3, Homo sapiens,#U26943; Caspase 4, Homo sapiens, #AAH17839; Caspase 5, Homo sapiens,#NP_(—)004338; Caspase 6, Homo sapiens, #NM_(—)001226 and NM_(—)032992;Caspase 7, Homo sapiens, #XM_(—)053352; Caspase 8, Homo sapiens,#NM_(—)001228; Caspase 9, Homo sapiens, #AB019197; Caspase 10, Homosapiens, #XP_(—)027991; Caspase 13, Homo sapiens, #AAC28380; Caspase 14,Homo sapiens, #NP_(—)036246; Caspase 1, Mus musculus, #BC008152; Caspase2, Mus musculus, #NM_(—)007610; Caspase 3, Mus musculus, #NM_(—)009810;Caspase 6, Mus musculus, #BC002022; Caspase 7, Mus musculus, #BC005428;Caspase 8, Mus musculus, #BC006737; Caspase 9, Mus musculus,#NM_(—)015733; Caspase 11, Mus musculus, #NM_(—)007609; Caspase 12, Musmusculus, #NM_(—)009808; Caspase 14, Mus musculus, #AF092997; and CED-3caspase, Caenorhabditis elegans, #AF210702); calpains (T. Lu et al.,(2002) Biochimica et Biophysica Acta 1590, 16-26)); a molecule thatdegrades components of pathogens, as described supra (for example andwithout limitation: proteases, including chymotrypsin, trypsin, orelastase; DNases, including restriction enzymes; RNases, including RNaseIII (Homo sapiens, #AF189011; Escherichia coli, #NP 417062,NC_(—)000913), RNt1p (Saccharomyces cerevisiae, #U27016), Pac1,(Schizosaccharomyces pombe, #X54998), or RNase L; glycosidases,including N-glycanase, endoglycosidase H, O-glycanase, endoglycosidaseF2, sialidase, or beta-galactosidase; or lipases, includingphospholipase A1, phospholipase A2, phospholipase C, or phospholipaseD); a molecule that inhibits or is toxic to a pathogen cell, asdescribed supra (including but not limited to penicillin, erythromycin,tetracycline, rifampin, amphotericin B, metronidazole, mefloquine, oranother molecule that inhibits pathogen functions).

An inducible promoter (for example and without limitation, one of thefollowing promoters as described herein: a dsRNA-inducible promoter;apoptosis-inducible promoter; unfolded protein response-induciblepromoter or endoplasmic reticulum-associated protein degradationresponse-inducible promoter; inflammatory response-inducible promoter;stress/heat shock-inducible promoter; promoter that can be induced bycytokines such as interferon alpha, interferon beta, or interferonomega; promoter that can be induced by cytokines such as interferongamma, interleukin 1, interleukin 2, interleukin 3, interleukin 4,interleukin 5, interleukin 6, interleukin 7, interleukin 9, interleukin12, or interleukin 15; or a drug-inducible promoter) can be operativelylinked with a polynucleotide sequence encoding an effector molecule thatcan act within the producing cell, between cells, or on or in othercells. The effector molecule can optionally include a cellular targetingtag or a protein uptake tag as described herein and/or a secretorysignal peptide, as will be understood by one of skill in the art. Inaddition to an optional tag or peptide, the effector molecule caninclude one or more of the following domains, for example and withoutlimitation: a chimeric molecule or agent as described herein, includingbut not limited to dsRNA-activated caspase,2′,5′-oligoadenylate-activated caspase, dsRNA-activated caspaseactivator, or 2′,5′-oligoadenylate-activated caspase activator; achimeric transcription factor as described herein; a molecule thatcontains two or more binding sites for a pathogen, pathogen component,or pathogen product as described herein; a molecule that executes,stimulates, or inhibits stress or inflammatory responses, as describedsupra (including but not limited to heat shock protein 70 (Hsp70: Homosapiens, #M11717, M15432, L12723, NM_(—)016299, NM_(—)005346,NM_(—)005345, NM_(—)002155, NM_(—)021979, AF093759; Mus musculus,#XM_(—)207065, XM_(—)128584, XM_(—)128585, XM_(—)110217, NM 015765,NM_(—)010481, NM_(—)008301, M76613), Hsc70 (Homo sapiens, #AF352832),Hsp90 (Homo sapiens, #M16660, NM_(—)005348, NM_(—)007355); Hsp40/Hdj-1(Homo sapiens, #X62421, NM_(—)006145, NM_(—)005880), Hsp60 (Homosapiens, #NM_(—)002156), Hsp47/CBP-2 (Homo sapiens, #D83174), Hsp100(Homo sapiens, #NM_(—)006660), Alpha-A-crystallin (Homo sapiens,#NM_(—)000394), Alpha-B-crystallin (Homo sapiens, #NM_(—)001885),Hsp27-1 (Homo sapiens, #NM_(—)001540), Hsp27-2 (Homo sapiens,#XM_(—)012054), cdc48 (S. Thoms (2002) FEBS Lett. 520, 107-110), heatshock factor 1 (HSF1: Homo sapiens, #NM_(—)005526, M64673; Mus musculus,#XM_(—)128055, X61753, Z49206; A. Mathew et al. (2001) Mol. Cell. Biol.21, 7163-7171; L. Pirkkala et al. (2001) FASEB J. 15, 1118-1131),constitutively active HSF1, RelA/p65 (Homo sapiens, #NM_(—)021975,Z22948, L19067; Mus musculus, #NM_(—)009045, AF199371), RelB (Homosapiens, #NM_(—)006509; Mus musculus, #NM_(—)009046, M83380), c-Rel(Homo sapiens, #X75042, NM_(—)002908; Mus musculus, #NM_(—)009044,X15842), p50/p105/NF-kappa B 1 (Homo sapiens, #NM_(—)003998, S76638,AF213884, AH009144; Mus musculus, #NM_(—)008689, AK052726, M57999),p52/p100/NF-kappa B 2 (Homo sapiens, #NM_(—)002502; Mus musculus,#AF155372, AF155373, NM_(—)019408), inhibitors of kappa B (I kappa B:Homo sapiens, #AY033600, NM_(—)020529; S. Ghosh and M. Karin (2002) Cell109, S81-S96), IKK1/I kappa B kinase alpha (1 alpha: Homo sapiens,#AF009225, AF080157), IKK2/I kappa B kinase beta (IKK beta: Homosapiens, #AF080158; Mus musculus, #AF026524, AF088910), or NEMO/I kappaB kinase gamma (IKK gamma: Homo sapiens, #AF261086, AF091453; Musmusculus, #AF069542)); a molecule that executes, stimulates, or inhibitsunfolded-protein-related or endoplasmic reticulum-associated proteindegradation-related responses, as described supra (including but notlimited to BiP/GRP78/SHPA5 (Homo sapiens, #AJ271729, AF216292, X87949,NM_(—)005347; Mus musculus, #NM_(—)022310), PKR-like endoplasmicreticulum kinase (PERK: Homo sapiens, #NP_(—)004827; Mus musculus,#AAD03337, NP_(—)034251), constitutively active PERK, IRE1 alpha (Homosapiens, #AF059198; Mus musculus, #AB031332, AF071777), constitutivelyactive IRE1 alpha, IRE1 beta (Homo sapiens, #AB047079), constitutivelyactive IRE1 beta, activating transcription factor 4 (ATF4: Homo sapiens,#NM_(—)001675; Mus musculus, #NM_(—)009716), activating transcriptionfactor 6 alpha or beta (ATF6 alpha or beta: Homo sapiens, #NM_(—)007348,AF005887, AB015856; Mus musculus, #XM_(—)129579), X-box binding protein1 (XBP1: Homo sapiens, #AB076383, AB076384; Mus musculus, #AF443192,AF027963, NM_(—)013842), CHOP-10/GADD153/DDIT3 (Homo sapiens,#NM_(—)004083; Mus musculus, #X67083, NM_(—)007837), site-1 protease(S1P: Homo sapiens, #NM_(—)003791; Mus musculus, #NM_(—)019709), site-2protease (S2P: Homo sapiens, #NM_(—)015884), presenilin-1 (Homo sapiens,#AH004968, AF416717; Mus musculus, #BC030409, NM_(—)008943, AF149111),TNF receptor-associated factor 2 (TRAF2: Homo sapiens, #NM_(—)021138,NM_(—)145718, Mus musculus, #XM_(—)203851, XM_(—)130119, L35303), orcJUN NH2-terminal kinases (JNKs: S. Oyadomari et al. (2002) Apoptosis 7,335-345)); a single-chain antibody or other molecule that binds to apathogen, pathogen component, or cellular component that directly orindirectly aids a pathogen, as described supra; a molecule that executesor stimulates complement pathway-related responses, as described supra,including but not limited to C3 alpha, C3 beta, factor B, factor D,properdin, C1q, C1r, C1s, C4, C2, C5, C6, C7, C8, C9, factor I, factorH, C1-INH, C4bp, S protein, clusterin, carboxypeptidase N, FHL-1, FHR-1,FHR-2, FHR-3, FHR-4, CR1, or DAF; a molecule that executes, stimulates,or inhibits toll-like-receptor-related responses, NOD-protein-relatedresponses, (including but not limited to Nod1/CARD4 (Homo sapiens,#AAD28350, AAD43922; N. Inohara et al. (1999) Journal of BiologicalChemistry 274, 14560-14567); Nod2, (Homo sapiens, #AAG33677, AAK70863,AAK70865, AAK70866, AAK70867, AAK70868; Y. Ogura et al. (2001) Journalof Biological Chemistry 276, 4812-4818; N. Inohara et al. (2003) Journalof Biological Chemistry, PMID: 12514169); Ipaf-1/CLAN/CARD12 (Homosapiens, #NM_(—)021209, AY035391; J.-L. Poyet et al. (2001) Journal ofBiological Chemistry 276, 28309-28313); CIITA (Homo sapiens, #AY084054,AY084055, AF410154, NM_(—)000246, X74301; M. W. Linhoff et al. (2001)Molecular and Cellular Biology 21, 3001-3011; A. Muhlethaler-Mottet etal. (1997) EMBO Journal 16, 2851-2860); NAIP (Homo sapiens, #U21912,U19251); Defcap/NAC/NALP1/CARD7 (Homo sapiens, #NM_(—)033004,NM_(—)033005, NM_(—)033006, NM_(—)033007, NM_(—)014922); NBS1/NALP2(Homo sapiens, #AF310106, NM_(—)017852); cryopyrin/CIAS1 (Homo sapiens,#AF410477, AF427617, AH011140, NM_(—)004895); RIP (Homo sapiens,#U50062; S. Grimm et al. (1996) Proc. Natl. Acad. Sci. USA 93,10923-10927; H. Hsu et al. (1996) Immunity 4, 387-396);Rip2/RICK/CARDIAK (Homo sapiens, #AF064824, AF078530; N. Inohara et al.(1998) Journal of Biological Chemistry 273, 18675; M. Thome et al.(1998) Current Biology 8, 885-888); and PKK (A. Muto et al. (2002)Journal of Biological Chemistry 277, 31871-31876)), pentraxin-relatedresponses, collectin-related responses, mannose-receptor-relatedresponses, scavenger receptor-related responses, or immune-relatedresponses, as described supra; a molecule that inhibits transportbetween the cytoplasm and the nucleus of a cell, as described supra(including but not limited to importin alpha 1 (Homo sapiens,#NM_(—)002266) with the importin beta binding domain (approximatelyamino acids 3-99) removed, importin alpha 3 (Homo sapiens,#NM_(—)002268) with the importin beta binding domain (approximatelyamino acids 3-94) removed, importin alpha 4 (Homo sapiens,#NM_(—)002267) with the importin beta binding domain (approximatelyamino acids 3-94) removed, importin alpha 5 (Homo sapiens, #U28386) withthe importin beta binding domain (approximately amino acids 3-94)removed, importin alpha 6 (Homo sapiens, #NM_(—)002269) with theimportin beta binding domain (approximately amino acids 3-94) removed,importin alpha 7 (Homo sapiens, #NM_(—)012316) with the importin betabinding domain (approximately amino acids 3-103) removed, importin alphawith the importin beta binding domain removed as described supra andalso with the last two armadillo repeats removed (Y. Miyamoto et al.(2002) EMBO Journal 21, 5833-5842), the autoinhibitory domain of animportin alpha mutated to have a higher than normal affinity forwild-type importin alpha (B. Catimel et al. (2001) Journal of BiologicalChemistry 276, 34189-34198), a modified importin alpha that does notenable nuclear import but still binds to one or more pathogen nuclearlocalization signals (NLSs) and does so preferably with a higheraffinity than it binds to cellular NLSs, the importin beta bindingdomain of importin alpha 1 (Homo sapiens, #NM_(—)002266, approximatelyamino acids 1-99), the importin beta binding domain of importin alpha 3(Homo sapiens, #NM_(—)002268, approximately amino acids 1-94), theimportin beta binding domain of importin alpha 4 (Homo sapiens,#NM_(—)002267, approximately amino acids 1-94), the importin betabinding domain of importin alpha 5 (Homo sapiens, #U28386, approximatelyamino acids 1-94), the importin beta binding domain of importin alpha 6(Homo sapiens, #NM_(—)002269, approximately amino acids 1-94), theimportin beta binding domain of importin alpha 7 (Homo sapiens,#NM_(—)012316, approximately amino acids 1-103), importin beta 1 (Homosapiens, #NM_(—)002265, #NP_(—)002256) modified to not bind nucleoporins(for example by deleting the region between HEAT-5 and HEAT-6(approximately amino acids 203-211) and the region between HEAT-6 andHEAT-7 (approximately amino acids 246-252) or by replacing those regionswith nonhomologous linker regions (Y. M. Chook and G. Blobel (2001)Current Opinion in Structural Biology 11, 703-715)), importin beta 1(Homo sapiens, #NM_(—)002265, #NP_(—)002256) modified to not bindimportin alpha (for example by deleting the acidic loopimportin-alpha-binding region spanning from approximately amino acid 333through approximately amino acid 343 (G. Cingolani et al. (1999) Nature399, 221-229)), a defective mutant of an exportin (I. G. Macara (2001)Microbiology and Molecular Biology Reviews 65, 570-594), a mutantp10/NTF2 that inhibits import by importin beta 1 (for example p10 D23A(C. M. Lane et al. (2000) Journal of Cell Biology 151, 321-331) or N77Y(B. B. Quimby et al. (2001) Journal of Biological Chemistry 276,38820-38829)), vesicuovirus matrix protein or a portion thereof thatinhibits nuclear import and/or nuclear export (J. M. Petersen et al.(2001) Proc. Natl. Acad. Sci. USA 98, 8590-8595; J. M. Petersen et al.(2000) Molecular and Cellular Biology 20, 8590-8601; C. von Kobbe et al.(2000) Molecular Cell 6, 1243-1252), a peptide that resembles theclassical nuclear localization signal of SV40 T antigen (E. Merle et al.(1999) Journal of Cellular Biochemistry 74, 628-637), another nuclearlocalization signal, peptides with FxFG repeats or GLFG repeats (R.Bayliss et al. (2002) Journal of Biological Chemistry 277, 50597-50606),leptomycin B, a mutant of Ran that interferes with nuclear import orexport (for example RanC4A (R. H. Kehlenbach et al. (2001) Journal ofBiological Chemistry 276, 14524-14531)), or a molecule that binds to apathogen or pathogen component or cellular component that is involved intransport between the cytoplasm and the nucleus of a cell (I. G. Macara(2001) Microbiology and Molecular Biology Reviews 65, 570-594; B.Ossareh-Nazari (2001) Traffic 2, 684-689)); a molecule that inhibitspathogenic prions (for example and without restriction, approximatelyamino acids 119-136 of hamster prion protein; J. Chabry et al. (1999)Journal of Virology 73, 6245-6250); a molecule that alters theproperties of the endocytic pathway, phagocytic pathway, endosomes,phagosomes, lysosomes, other intracellular compartments, or vesiculartrafficking to produce an anti-pathogen effect, as described supra(including but not limited to dynamin-1 mutant K44A (M. Huber et al.(2001) Traffic 2, 727-736; particularly when overexpressed), cellubrevin(R. A. Fratti et al. (2002) Journal of Biological Chemistry 277,17320-17326; particularly when overexpressed), Salmonella SpiC protein(NCBI Accession #U51927), a defective mutant of TassC (A. H. Lee et al.(2002) Cell. Microbiol. 4, 739-750), other vesicular traffickinginhibitors as will be understood by one of skill in the art, Nramp1 (P.Cuellar-Mata et al. (2002) Journal of Biological Chemistry 277,2258-2265; C. Frehel et al. (2002) Cellular Microbiology 4, 541-556; D.J. Hackam et al. (1998) J. Exp. Med. 188, 351-364; particularly whenoverexpressed), NADPH oxidase subunits or cofactors (P. V. Vignais(2002) Cell. Mol. Life Sci. 59, 1428-1459; particularly whenoverexpressed), NOS2 nitric oxide synthase (J. D. MacMicking et al.(1997) Proc. Natl. Acad. Sci. USA 94, 5243-5248; particularly whenoverexpressed), human papillomavirus 16 E5 protein (NCBI Accession#W5WLHS), bafilomycin A1, a single-chain antibody or other molecule thatbinds to vacuolar ATPase subunit a (S. B. Sato and S. Toyama (1994) J.Cell. Biol. 127, 39-53; preferably a1 or a2), antisense oligonucleotidesthat inhibit vacuolar ATPase subunits (J. E. Strasser et al. (1999)Journal of Immunology 162, 6148-6154), a peptide composed ofapproximately the 78 amino-terminal amino acids of vacuolar H+-ATPasesubunit E (M. Lu et al. (2002) Journal of Biological Chemistry 277,38409-38415), A2-cassette mutant of vacuolar H+-ATPase subunit A (N.Hernando et al. (1999) Eur. J. Biochem. 266, 293-301), a defectivemutant of subunit a1 or a2 of vacuolar H+-ATPase (S. Kawasaki-Nishi etal. (2001) Proc. Natl. Acad. Sci. USA 98, 12397-12402; S. Kawasaki-Nishiet al. (2001) 276, 47411-47420; T. Nishi and M. Forgac (2000) J. Biol.Chem. 275, 6824-6830; S. B. Peng et al. (1999) J. Biol. Chem. 274,2549-2555; T. Toyomura et al. (2000) J. Biol. Chem. 275, 8760-8765),overexpression of the C and/or H subunits of vacuolar H+-ATPase subunitE (K. K. Curtis and P. M. Kane (2002) Journal of Biological Chemistry277, 2716-2724), other defective vacuolar ATPase subunit or portion of asubunit (examples of wild-type human vacuolar ATPase subunits that canbe made defective for anti-pathogen effects will be understood by one ofskill in the art, and include, without limitation, those vacuolar ATPasesubunits with Accession numbers: NM_(—)004231, NM_(—)130463,NM_(—)015994, NM_(—)001694, NM_(—)004047, NM_(—)001696, NM_(—)004691,NM_(—)001695, NM_(—)001693, NM_(—)001690, NM_(—)020632, NM_(—)004888));a molecule that executes, stimulates, or inhibits ubiquitin proteasomedegradative pathway-related responses, as described supra (including butnot limited to CHIP (D. M. Cyr et al. (2002) Trends Biochem. Sci. 27,368-375; J. Demand et al. (2001) Curr. Biol. 11, 1569-1577; S. Murata etal. (2001) EMBO Rep. 2, 1133-1138; particularly when overexpressed),Fbx2 (Y. Yoshida et al. (2002) Nature 418, 438-442; particularly whenoverexpressed), molecules that ubiquitinate pathogens or pathogencomponents or cellular components that assist pathogens as will beunderstood by one of skill in the art (P. Zhou et al. (2000) Mol. Cell6, 751-756; K. M. Sakamoto et al. (2001) Proc. Natl. Acad. Sci. USA 98,8554-8559; N. Zheng et al. (2000) Cell 102, 533-539; D. Oyake et al.(2002) Biochemical and Biophysical Research Communications 295,370-375), or inhibitors of ubiquitination or proteasomes (J. Myung etal. (2001) Medicinal Research Reviews 21, 245-273; G. Lennox et al.(1988) Neurosci. Lett. 94, 211-217; N. F. Bence et al. (2001) Science292, 1552-1555; for example lactacystin or epoxomicin)); a molecule thatexecutes, stimulates, or inhibits defensin-related responses, asdescribed supra, including but not limited to alpha defensins, betadefensins, theta defensins, plant defensins, or arthropod defensins; amolecule that executes, stimulates, or inhibits cathelicidin-relatedresponses, as described supra, including but not limited tohCAP-18/LL-37, CRAMP, Bac4, OaBac5; prophenin-1, protegrin-1, or PR-39;a molecule that executes, stimulates, or inhibits chemokine-related orthrombocidin-related responses, as described supra, including but notlimited to CC chemokines, CXC chemokines, C chemokines, CX3C chemokines,CC chemokine receptors, CXC chemokine receptors, C chemokine receptors,CX3C chemokine receptors, JAK proteins, STAT proteins, fibrinopeptide A,fibrinopeptide B, or thymosin beta 4; a molecule that executes,stimulates, or inhibits interferon-related or cytokine-relatedresponses, as described supra (including but not limited tointerferon-alpha (Homo sapiens, #NM_(—)002169, NM_(—)021002, J00207; Musmusculus, #NM_(—)010502, NM_(—)010503, NM_(—)010507, NM_(—)008333,M68944, M13710); interferon-beta (Homo sapiens, #M25460, NM_(—)002176;Mus musculus, #NM_(—)010510); interferon-gamma (Homo sapiens,#NM_(—)000619, J00219; Mus musculus, #M28621); interferon-delta;interferon-tau; interferon-omega (Homo sapiens, #NM_(—)002177);interleukin 1 (IL-1: Homo sapiens, #NM_(—)000575, NM_(—)012275,NM_(—)019618, NM_(—)000576, NM_(—)014439; Mus musculus, #NM_(—)019450,NM_(—)019451, AF230378); interleukin 2 (IL-2: Homo sapiens,#NM_(—)000586); interleukin 3 (IL-3: Homo sapiens, #NM_(—)000588; Musmusculus, #A02046); interleukin 4 (IL-4: Homo sapiens, #NM_(—)000589,NM_(—)172348; Mus musculus, #NM_(—)021283); interleukin 5 (IL-5: Homosapiens, #NM_(—)000879; Mus musculus, #NM_(—)010558); interleukin 6(IL-6: Homo sapiens, #NM_(—)000600; Mus musculus, #NM_(—)031168);interleukin 7 (IL-7: Homo sapiens, #NM_(—)000880, AH006906; Musmusculus, #NM_(—)008371); interleukin 9 (IL-9: Homo sapiens,#NM_(—)000590); interleukin 12 (IL-12: Homo sapiens, #NM_(—)000882,NM_(—)002187; Mus musculus, #NM_(—)008351, NM_(—)008352); interleukin 15(IL-15: Homo sapiens, #NM_(—)172174, NM_(—)172175, NM_(—)000585; Musmusculus, #NM_(—)008357); cytokine receptors and related signalingmolecules (W. E. Paul (ed.), Fundamental Immunology (4th ed.,Lippincott-Raven, Philadelphia, 1999), Chapters 21 and 22); interferontype I receptor subunit 1 (IFNAR1: Homo sapiens, #NM_(—)000629; Musmusculus, #NM_(—)010508); interferon type I receptor subunit 2 (IFNAR2:Homo sapiens, #NM_(—)000874; Mus musculus, #NM_(—)010509); janus kinase1 (JAK1: Homo sapiens, #NP_(—)002218; Mus musculus, #NP_(—)666257);janus kinase 2 (JAK2: Homo sapiens, #AAC23653, AAC23982, NP_(—)004963;Mus musculus, #NP_(—)032439, AAN62560); JAK3; Tyk2; signal transducerand activator of transcription 1 (STAT1: Homo sapiens, #NM_(—)007315,NM_(—)139266; Mus musculus, #U06924); signal transducer and activator oftranscription 2 (STAT2: Homo sapiens, #NM_(—)005419; Mus musculus,AF206162); STAT3; STAT4; STAT5; STAT6; interferon-stimulated gene factor3 gamma (ISGF3 gamma: Homo sapiens, #Q00978, NM_(—)006084; Mus musculus,#NM_(—)008394) interferon regulatory factor 1 (IRF1: Homo sapiens,#NM_(—)002198, P10914; Mus musculus, #NM_(—)008390); interferonregulatory factor 3 (IRF3: Homo sapiens, #NM_(—)001571, Z56281; Musmusculus, #NM_(—)016849, U75839, U75840); interferon regulatory factor 5(IRF5: Homo sapiens, #Q13568, U51127; Mus musculus, #AAB81997,NP_(—)036187); interferon regulatory factor 6 (IRF6: Homo sapiens,#AF027292, NM_(—)006147; Mus musculus, #U73029); interferon regulatoryfactor 7 (IRF7: Homo sapiens, #U53830, U53831, U53832, AF076494, U73036;Mus musculus, #NM_(—)016850, U73037); interferon regulatory factor 8(IRF8); a constitutively active interferon regulatory factor; proteinkinase R (PKR: Homo sapiens, #AAC50768; Mus musculus, #Q03963; S.Nanduri et al. (1998) EMBO J. 17, 5458-5465); 2′,5′-oligoadenylatesynthetases (Homo sapiens forms including #P00973, P29728, AAD28543; Musmusculus forms including P11928; S. Y. Desai et al. (1995) J. Biol.Chem. 270, 3454-3461); RNase L (Homo sapiens, #CAA52920); );promyelocytic leukemia protein (PML: W. V. Bonilla et al. (2002) Journalof Virology 76, 3810-3818); p56 or related proteins (J. Guo et al.(2000) EMBO Journal 19, 6891-6899; G. C. Sen (2000) Seminars in CancerBiology 10, 93-101); p200 or related proteins (G. C. Sen (2000) Seminarsin Cancer Biology 10, 93-101); ADAR1 (Homo sapiens, #U18121; Musmusculus, #NP_(—)062629); Mx1 (Homo sapiens, #NM_(—)002462); or Mx2(Homo sapiens, #NM_(—)002463)); a molecule that inhibits budding orrelease of pathogens from an infected cell, as described supra(including but not limited to Hrs, particularly when overexpressed (N.Bishop et al. (2002) Journal of Cell Biology 157, 91-101; L. Chin et al.(2001) Journal of Biological Chemistry 276, 7069-7078; C. Raiborg et al.(2002) Nature Cell Biology 4, 394-398); defective Vps4 mutants such asK173Q or E228Q, particularly when overexpressed (J. E. Garrus et al.(2001) Cell 107, 55-65); small interfering RNA that inhibits Tsg101expression (N. Bishop et al. (2002) Journal of Cell Biology 157, 91-101;J. E. Garrus et al. (2001) Cell 107, 55-65); truncated AP-50 consistingof approximately amino acids 121-435, or other defective mutant ofAP-50, particularly when overexpressed (B. A. Puffer et al. (1998)Journal of Virology 72, 10218-10221); WW-domain-containing fragment ofLDI-1, Nedd4, Yes-associated protein, KIAA0439 gene product, or otherdefective Nedd4-related proteins, particularly when overexpressed (A.Kikonyogo et al. (2001) Proc. Natl. Acad. Sci. USA 98, 11199-11204; A.Patnaik and J. W. Wills (2002) Journal of Virology 76, 2789-2795); apeptide consisting of the HIV p6 Gag PTAPP-motif-containing late (L)domain (L. VerPlank et al. (2001) Proc. Natl. Acad. Sci. USA 98,7724-7729) or other viral late (L) domain containing PTAP, PSAP, PPXY,YPDL, or YXXL motifs (J. Martin-Serrano et al. (2001) Nature Medicine 7,1313-1319; A. Patnaik and J. W. Wills (2002) Journal of Virology 76,2789-2795); amino acids 1-167 of Tsg101, TSG-5′ fragment of Tsg101, orsimilar amino-terminal fragment of Tsg101, particularly whenoverexpressed (D. G. Demirov et al. (2002) Proc. Natl. Acad. Sci. USA99, 955-9601; E. L. Myers and J. F. Allen (2002) Journal of Virology 76,11226-11235); a mutant of Tsg101 (M. Babst et al. (2000) Traffic 1,248-258; L. VerPlank et al. (2001) Proc. Natl. Acad. Sci. USA 98,7724-7729; J. Martin-Serrano et al. (2001) Nature Medicine 7, 1313-1319;O. Pornillos et al. (2002) EMBO Journal 21, 2397-2406) with reducedcapacity to aid viral budding; a casein kinase 2 (CK2) inhibitor, suchas the peptide RRADDSDDDDD (SEQ ID NO: 472)(E. K. Hui and D. P. Nayak(2002) Journal of General Virology 83, 3055-3066); or G proteinsignalling inhibitors (E. K. Hui and D. P. Nayak (2002) Journal ofGeneral Virology 83, 3055-3066); a molecule that binds to a cellular orpathogen molecule (for example to one or more of the followingmolecules: Tsg101, Vps4, casein kinase 2, Hrs, hVps28, Eap30, Eap20,Eap45, Chmp1, Chmp2, Chmp3, Chmp4, Chmp5, Chmp6, AP-50, Nedd4-relatedproteins, WW-domain-containing proteins, or L-domain-containingproteins; O. Pornillos et al. (2002) TRENDS in Cell Biology 12, 569-579;P. Gomez-Puertas et al. (2000) Journal of Virology 74, 11538-11547; E.Katz et al. (2002) Journal of Virology 76, 11637-11644) that is involvedin budding or release of pathogens from an infected cell); a moleculethat makes a cell more receptive to apoptosis signals, as describedsupra (including but not limited to p53 (Homo sapiens, #AAF36354 throughAAF36382; Mus musculus, #AAC05704, AAD39535, AAF43275, AAF43276,AAK53397); Bax (Homo sapiens, #NM_(—)004324); Bid (Homo sapiens,#NM_(—)001196); apoptotic protease activating factor 1 (Apaf-1: Homosapiens, #NM_(—)013229, NM_(—)001160; Mus musculus, #NP_(—)033814);Fas/CD95 (Homo sapiens, #AAC16236, AAC16237; Mus musculus, #AAG02410);TNF receptors (Homo sapiens, #NP_(—)001056; V. Baud and M. Karin (2001)TRENDS in Cell Biology 11, 372-377; U. Sartorius et al. (2001)Chembiochem 2, 20-29); FLICE-activated death domain (FADD: Homo sapiens,#U24231; Mus musculus, #NM_(—)010175); TRADD (Homo sapiens,#NP_(—)003780, CAC38018); Smac/DIABLO (Homo sapiens, #NM_(—)019887);caspases (including but not restricted to Caspase 1, Homo sapiens,#NM_(—)001223; Caspase 2, Homo sapiens, #NM_(—)032982, NM_(—)001224,NM_(—)032983, and NM_(—)032984; Caspase 3, Homo sapiens, #U26943;Caspase 4, Homo sapiens, #AAH17839; Caspase 5, Homo sapiens,#NP_(—)004338; Caspase 6, Homo sapiens, #NM_(—)001226 and NM_(—)032992;Caspase 7, Homo sapiens, #XM_(—)053352; Caspase 8, Homo sapiens,#NM_(—)001228; Caspase 9, Homo sapiens, #AB019197; Caspase 10, Homosapiens, #XP_(—)027991; Caspase 13, Homo sapiens, #AAC28380; Caspase 14,Homo sapiens, #NP_(—)036246; Caspase 1, Mus musculus, #BC008152; Caspase2, Mus musculus, #NM_(—)007610; Caspase 3, Mus musculus, #NM_(—)009810;Caspase 6, Mus musculus, #BC002022; Caspase 7, Mus musculus, #BC005428;Caspase 8, Mus musculus, #BC006737; Caspase 9, Mus musculus,#NM_(—)015733; Caspase 11, Mus musculus, #NM_(—)007609; Caspase 12, Musmusculus, #NM_(—)009808; Caspase 14, Mus musculus, #AF092997; and CED-3caspase, Caenorhabditis elegans, #AF210702); calpains (T. Lu et al.,(2002) Biochimica et Biophysica Acta 1590, 16-26)); a molecule thatdegrades components of pathogens, as described supra (for example:proteases, including but not limited to chymotrypsin, trypsin, orelastase; DNases, including but not limited to restriction enzymes;RNases, including but not limited to RNase III (Homo sapiens, #AF189011;Escherichia coli, #NP_(—)417062, NC_(—)000913), RNt1p (Saccharomycescerevisiae, #U27016), Pac1, (Schizosaccharomyces pombe, #X54998), orRNase L; glycosidases, including but not limited to N-glycanase,endoglycosidase H, O-glycanase, endoglycosidase F2, sialidase, orbeta-galactosidase; or lipases, including but not limited tophospholipase A1, phospholipase A2, phospholipase C, or phospholipaseD); a molecule that inhibits or is toxic to a pathogen cell, asdescribed supra (including but not limited to penicillin, erythromycin,tetracycline, rifampin, amphotericin B, metronidazole, mefloquine, oranother molecule that inhibits pathogen functions).

A chimeric molecule or agent of the invention can be a messenger RNA(mRNA) molecule that only encodes a functional anti-pathogen domain ormolecular structure if the mRNA is naturally spliced within a cell thatis undergoing an unfolded protein response or endoplasmicreticulum-associated protein degradation response. For example andwithout limitation, the mRNA can include within its protein encodingsequence the 5′ and 3′ splice sites from the intron that is removed fromXBP1 mRNA by activated IRE1 alpha (H. Yoshida et al. (2001) Cell 107,881-891; K. Lee et al. (2002) Genes & Development 16, 452-466; W.Tirasophon et al. (2000) Genes & Development 14, 2725-2736) withnucleotides between the splice sites such that the mRNA encodes ananti-pathogen molecule when the mRNA is spliced by activated IRE1 alphabut only a nonfunctional version of the anti-pathogen molecule withnonsense or frameshift mutations when the mRNA is unspliced, as will beunderstood by one of skill in the art. The mRNA can encode one or moreof the following effector molecules, for example and without limitation:a chimeric molecule or agent as described herein, including but notlimited to dsRNA-activated caspase, 2′,5′-oligoadenylate-activatedcaspase, dsRNA-activated caspase activator, or2′,5′-oligoadenylate-activated caspase activator; a chimerictranscription factor as described herein; a molecule that contains twoor more binding sites for a pathogen, pathogen component, or pathogenproduct as described herein; an antisense polynucleotide or smallinterfering RNA (G. M. Barton and R. Medzhitov (2002) Proc. Natl. Acad.Sci. USA 99, 14943-14945) that inhibits expression of a pathogen gene ora host gene that aids a pathogen; a molecule that executes, stimulates,or inhibits stress or inflammatory responses, as described supra(including but not limited to heat shock protein 70 (Hsp70: Homosapiens, #M11717, M15432, L12723, NM_(—)016299, NM_(—)005346,NM_(—)005345, NM_(—)002155, NM_(—)021979, AF093759; Mus musculus,#XM_(—)207065, XM_(—)128584, XM_(—)128585, XM_(—)110217, NM_(—)015765,NM_(—)010481, NM_(—)008301, M76613), Hsc70 (Homo sapiens, #AF352832),Hsp90 (Homo sapiens, #M16660, NM_(—)005348, NM_(—)007355); Hsp40/Hdj-1(Homo sapiens, #X62421, NM_(—)006145, NM_(—)005880), Hsp60 (Homosapiens, #NM_(—)002156), Hsp47/CBP-2 (Homo sapiens, #D83174), Hsp100(Homo sapiens, #NM_(—)006660), Alpha-A-crystallin (Homo sapiens,#NM_(—)000394), Alpha-B-crystallin (Homo sapiens, #NM_(—)001885),Hsp27-1 (Homo sapiens, #NM_(—)001540), Hsp27-2 (Homo sapiens,#XM_(—)012054), cdc48 (S. Thoms (2002) FEBS Lett. 520, 107-110), heatshock factor 1 (HSF1: Homo sapiens, #NM_(—)005526, M64673; Mus musculus,#XM_(—)128055, X61753, Z49206; A. Mathew et al. (2001) Mol. Cell. Biol.21, 7163-7171; L. Pirkkala et al. (2001) FASEB J. 15, 1118-1131),constitutively active HSF1, RelA/p65 (Homo sapiens, #NM_(—)021975,Z22948, L119067; Mus musculus, #NM_(—)009045, AF199371), RelB (Homosapiens, #NM_(—)006509; Mus musculus, #NM_(—)009046 μM83380), c-Rel(Homo sapiens, #X75042, NM_(—)002908; Mus musculus, #NM_(—)009044,X15842), p50/p105/NF-kappa B 1 (Homo sapiens, #NM_(—)003998, S76638,AF213884, AH009144; Mus musculus, #NM_(—)008689, AK052726, M57999),p52/p100/NF-kappa B 2 (Homo sapiens, #NM_(—)002502; Mus musculus,#AF155372, A-F155373, NM_(—)019408), inhibitors of kappa B (I kappa B:Homo sapiens, #AY033600, NM_(—)020529; S. Ghosh and M. Karin (2002) Cell109, S811-S96), IKK1/I kappa B kinase alpha (IKK alpha: Homo sapiens,#AF009225, AF080157), IKK2/I kappa B kinase beta (IKK beta: Homosapiens, #AF080158; Mus musculus, #AF026524, AF088910), or NEMO/I kappaB kinase gamma (IKK gamma: Homo sapiens, #AF261086, AF091453; Musmusculus, #AF069542)); a molecule that executes, stimulates, or inhibitsunfolded-protein-related or endoplasmic reticulum-associated proteindegradation-related responses, as described supra (including but notlimited to BiP/GRP78/SHPA5 (Homo sapiens, #AJ271729, AF216292, X87949,NM_(—)005347; Mus musculus, #NM_(—)022310), PKR-like endoplasmicreticulum kinase (PERK: Homo sapiens, #NP_(—)004827; Mus musculus,#AAD03337, NP_(—)034251), constitutively active PERK, IRE1 alpha (Homosapiens, #AF059198; Mus musculus, #AB031332, AF071777), constitutivelyactive IRE1 alpha, IRE1 beta (Homo sapiens, #AB047079), constitutivelyactive IRE1 beta, activating transcription factor 4 (ATF4: Homo sapiens,#NM_(—)001675; Mus musculus, #NM_(—)009716), activating transcriptionfactor 6 alpha or beta (ATF6 alpha or beta: Homo sapiens, #NM_(—)007348,AF005887, AB015856; Mus musculus, #XM_(—)129579), X-box binding protein1 (XBP1: Homo sapiens, #AB076383, AB076384; Mus musculus, #AF443192,AF027963, NM 013842), CHOP-10/GADD153/DDIT3 (Homo sapiens,#NM_(—)004083; Mus musculus, #X67083, NM_(—)007837), site-1 protease(S1P: Homo sapiens, #NM_(—)003791; Mus musculus, #NM_(—)019709), site-2protease (S2P: Homo sapiens, #NM_(—)015884), presenilin-1 (Homo sapiens,#AH004968, AF416717; Mus musculus, #BC030409, NM_(—)008943, AF149111),TNF receptor-associated factor 2 (TRAF2: Homo sapiens, #NM_(—)021138,NM_(—)145718, Mus musculus, #XM_(—)203851, XM_(—)130119, L35303), orcJUN NH2-terminal kinases (JNKs: S. Oyadomari et al. (2002) Apoptosis 7,335-345)); a single-chain antibody or other molecule that binds to apathogen, pathogen component, or cellular component that directly orindirectly aids a pathogen, as described supra; a molecule that executesor stimulates complement pathway-related responses, as described supra,including but not limited to C3 alpha, C3 beta, factor B, factor D,properdin, C1q, C1r, C1s, C4, C2, C5, C6, C7, C8, C9, factor I, factorH, C1-INH, C4 bp, S protein, clusterin, carboxypeptidase N, FHL-1,FHR-1, FHR-2, FHR-3, FHR-4, CR1, or DAF; a molecule that executes,stimulates, or inhibits toll-like-receptor-related responses,NOD-protein-related responses, (including but not limited to Nod1/CARD4(Homo sapiens, #AAD28350, AAD43922; N. Inohara et al. (1999) Journal ofBiological Chemistry 274, 14560-14567); Nod2, (Homo sapiens, #AAG33677,AAK70863, AAK70865, AAK70866, AAK70867, AAK70868; Y. Ogura et al. (2001)Journal of Biological Chemistry 276, 4812-4818; N. Inohara et al. (2003)Journal of Biological Chemistry, PMID: 12514169); Ipaf-1/CLAN/CARD12(Homo sapiens, #NM_(—)021209, AY035391; J.-L. Poyet et al. (2001)Journal of Biological Chemistry 276, 28309-28313); CIITA (Homo sapiens,#AY084054, AY084055, AF410154, NM_(—)000246, X74301; M. W. Linhoff etal. (2001) Molecular and Cellular Biology 21, 3001-3011; A.Muhlethaler-Mottet et al. (1997) EMBO Journal 16, 2851-2860); NAIP (Homosapiens, #U21912, U19251); Defcap/NAC/NALP1/CARD7 (Homo sapiens,#NM_(—)033004, NM_(—)033005, NM_(—)033006, NM_(—)033007, NM_(—)014922);NBS1/NALP2 (Homo sapiens, #AF310106, NM_(—)017852); cryopyrin/CIAS1(Homo sapiens, #AF410477, AF427617, AH011140, NM_(—)004895); RIP (Homosapiens, #U50062; S. Grimm et al. (1996) Proc. Natl. Acad. Sci. USA 93,10923-10927; H. Hsu et al. (1996) Immunity 4, 387-396);Rip2/RICK/CARDIAK (Homo sapiens, #AF064824, AF078530; N. Inohara et al.(1998) Journal of Biological Chemistry 273, 18675; M. Thome et al.(1998) Current Biology 8, 885-888); and PKK (A. Muto et al. (2002)Journal of Biological Chemistry 277, 31871-31876)), pentraxin-relatedresponses, collectin-related responses, mannose-receptor-relatedresponses, scavenger receptor-related responses, or immune-relatedresponses, as described supra; a molecule that inhibits transportbetween the cytoplasm and the nucleus of a cell, as described supra(including but not limited to importin alpha 1 (Homo sapiens,#NM_(—)002266) with the importin beta binding domain (approximatelyamino acids 3-99) removed, importin alpha 3 (Homo sapiens,#NM_(—)002268) with the importin beta binding domain (approximatelyamino acids 3-94) removed, importin alpha 4 (Homo sapiens,#NM_(—)002267) with the importin beta binding domain (approximatelyamino acids 3-94) removed, importin alpha 5 (Homo sapiens, #U28386) withthe importin beta binding domain (approximately amino acids 3-94)removed, importin alpha 6 (Homo sapiens, #NM_(—)002269) with theimportin beta binding domain (approximately amino acids 3-94) removed,importin alpha 7 (Homo sapiens, #NM_(—)012316) with the importin betabinding domain (approximately amino acids 3-103) removed, importin alphawith the importin beta binding domain removed as described supra andalso with the last two armadillo repeats removed (Y. Miyamoto et al.(2002) EMBO Journal 21, 5833-5842), the autoinhibitory domain of animportin alpha mutated to have a higher than normal affinity forwild-type importin alpha (B. Catimel et al. (2001) Journal of BiologicalChemistry 276, 34189-34198), a modified importin alpha that does notenable nuclear import but still binds to one or more pathogen nuclearlocalization signals (NLSs) and does so preferably with a higheraffinity than it binds to cellular NLSs as will be understood by one ofskill in the art, the importin beta binding domain of importin alpha 1(Homo sapiens, #NM_(—)002266, approximately amino acids 1-99), theimportin beta binding domain of importin alpha 3 (Homo sapiens,#NM_(—)002268, approximately amino acids 1-94), the importin betabinding domain of importin alpha 4 (Homo sapiens, #NM_(—)002267,approximately amino acids 1-94), the importin beta binding domain ofimportin alpha 5 (Homo sapiens, #U28386, approximately amino acids1-94), the importin beta binding domain of importin alpha 6 (Homosapiens, #NM_(—)002269, approximately amino acids 1-94), the importinbeta binding domain of importin alpha 7 (Homo sapiens, #NM_(—)012316,approximately amino acids 1-103), importin beta 1 (Homo sapiens,#NM_(—)002265, #NP_(—)002256) modified to not bind nucleoporins (forexample by deleting the region between HEAT-5 and HEAT-6 (approximatelyamino acids 203-211) and the region between HEAT-6 and HEAT-7(approximately amino acids 246-252) or by replacing those regions withnonhomologous linker regions (Y. M. Chook and G. Blobel (2001) CurrentOpinion in Structural Biology 11, 703-715)), importin beta 1 (Homosapiens, #NM_(—)002265, #NP_(—)002256) modified to not bind importinalpha (for example by deleting the acidic loop importin-alpha-bindingregion spanning from approximately amino acid 333 through approximatelyamino acid 343 (G. Cingolani et al. (1999) Nature 399, 221-229)), adefective mutant of an exportin (I. G. Macara (2001) Microbiology andMolecular Biology Reviews 65, 570-594), a mutant p10/NTF2 that inhibitsimport by importin beta 1 (for example p10 D23A (C. M. Lane et al.(2000) Journal of Cell Biology 151, 321-331) or N77Y (B. B. Quimby etal. (2001) Journal of Biological Chemistry 276, 38820-38829)),vesicuovirus matrix protein or a portion thereof that inhibits nuclearimport and/or nuclear export (J. M. Petersen et al. (2001) Proc. Natl.Acad. Sci. USA 98, 8590-8595; J. M. Petersen et al. (2000) Molecular andCellular Biology 20, 8590-8601; C. von Kobbe et al. (2000) MolecularCell 6, 1243-1252), a peptide that resembles the classical nuclearlocalization signal of SV40 T antigen (E. Merle et al. (1999) Journal ofCellular Biochemistry 74, 628-637), another nuclear localization signal,peptides with FxFG repeats or GLFG repeats (R. Bayliss et al. (2002)Journal of Biological Chemistry 277, 50597-50606), leptomycin B, amutant of Ran that interferes with nuclear import or export (for exampleRanC4A (R. H. Kehlenbach et al. (2001) Journal of Biological Chemistry276, 14524-14531)), or a molecule that binds to a pathogen or pathogencomponent or cellular component that is involved in transport betweenthe cytoplasm and the nucleus of a cell (I. G. Macara (2001)Microbiology and Molecular Biology Reviews 65, 570-594; B.Ossareh-Nazari (2001) Traffic 2, 684-689)); a molecule that inhibitspathogenic prions (for example and without restriction, approximatelyamino acids 119-136 of hamster prion protein; J. Chabry et al. (1999)Journal of Virology 73, 6245-6250); a molecule that alters theproperties of the endocytic pathway, phagocytic pathway, endosomes,phagosomes, lysosomes, other intracellular compartments, or vesiculartrafficking to produce an anti-pathogen effect, as described supra(including but not limited to dynamin-1 mutant K44A (M. Huber et al.(2001) Traffic 2, 727-736; particularly when overexpressed), cellubrevin(R. A. Fratti et al. (2002) Journal of Biological Chemistry 277,17320-17326; particularly when overexpressed), Salmonella SpiC protein(NCBI Accession #U51927), a defective mutant of TassC (A. H. Lee et al.(2002) Cell. Microbiol. 4, 739-750), other vesicular traffickinginhibitors as will be understood by one of skill in the art, Nramp1 (P.Cuellar-Mata et al. (2002) Journal of Biological Chemistry 277,2258-2265; C. Frehel et al. (2002) Cellular Microbiology 4, 541-556; D.J. Hackam et al. (1998) J. Exp. Med. 188, 351-364; particularly whenoverexpressed), NADPH oxidase subunits or cofactors (P. V. Vignais(2002) Cell. Mol. Life Sci. 59, 1428-1459; particularly whenoverexpressed), NOS2 nitric oxide synthase (J. D. MacMicking et al.(1997) Proc. Natl. Acad. Sci. USA 94, 5243-5248; particularly whenoverexpressed), human papillomavirus 16 E5 protein (NCBI Accession#W5WLHS), bafilomycin A1, a single-chain antibody or other molecule thatbinds to vacuolar ATPase subunit a (S. B. Sato and S. Toyama (1994) J.Cell. Biol. 127, 39-53; preferably a1 or a2,), antisenseoligonucleotides that inhibit vacuolar ATPase subunits (J. E. Strasseret al. (1999) Journal of Immunology 162, 6148-6154;), a peptide composedof approximately the 78 amino-terminal amino acids of vacuolar H+-ATPasesubunit E (M. Lu et al. (2002) Journal of Biological Chemistry 277,38409-38415), A2-cassette mutant of vacuolar H+-ATPase subunit A (N.Hernando et al. (1999) Eur. J. Biochem. 266, 293-301), a defectivemutant of subunit a1 or a2 of vacuolar H+-ATPase (S. Kawasaki-Nishi etal. (2001) Proc. Natl. Acad. Sci. USA 98, 12397-12402; S. Kawasaki-Nishiet al. (2001) 276, 47411-47420; T. Nishi and M. Forgac (2000) J. Biol.Chem. 275, 6824-6830; S. B. Peng et al. (1999) J. Biol. Chem. 274,2549-2555; T. Toyomura et al. (2000) J. Biol. Chem. 275, 8760-8765),overexpression of the C and/or H subunits of vacuolar H+-ATPase subunitE (K. K. Curtis and P. M. Kane (2002) Journal of Biological Chemistry277, 2716-2724), other defective vacuolar ATPase subunit or portion of asubunit (examples of wild-type human vacuolar ATPase subunits that canbe made defective for anti-pathogen effects will be understood by one ofskill in the art, and include, without limitation, those vacuolar ATPasesubunits with Accession numbers: NM_(—)004231, NM_(—)130463,NM_(—)015994, NM_(—)001694, NM_(—)004047, NM_(—)001696, NM_(—)004691,NM_(—)001695, NM_(—)001693, NM_(—)001690, NM_(—)020632, NM_(—)004888));a molecule that executes, stimulates, or inhibitsubiquitin-proteasome-degradative-pathway-related responses, as describedsupra (including but not limited to CHIP (D. M. Cyr et al. (2002) TrendsBiochem. Sci. 27, 368-375; J. Demand et al. (2001) Curr. Biol. 11,1569-1577; S. Murata et al. (2001) EMBO Rep. 2, 1133-1138; particularlywhen overexpressed), Fbx2 (Y. Yoshida et al. (2002) Nature 418, 438-442;particularly when overexpressed), molecules that ubiquitinate pathogensor pathogen components or cellular components that assist pathogens aswill be understood by one of skill in the art (P. Zhou et al. (2000)Mol. Cell 6, 751-756; K. M. Sakamoto et al. (2001) Proc. Natl. Acad.Sci. USA 98, 8554-8559; N. Zheng et al. (2000) Cell 102, 533-539; D.Oyake et al. (2002) Biochemical and Biophysical Research Communications295, 370-375), or inhibitors of ubiquitination or proteasomes (J. Myunget al. (2001) Medicinal Research Reviews 21, 245-273; G. Lennox et al.(1988) Neurosci. Lett. 94, 211-217; N. F. Bence et al. (2001) Science292, 1552-1555; for example lactacystin or epoxomicin)); a molecule thatexecutes, stimulates, or inhibits defensin-related responses, asdescribed supra, including but not limited to alpha defensins, betadefensins, theta defensins, plant defensins, or arthropod defensins; amolecule that executes, stimulates, or inhibits cathelicidin-relatedresponses, as described supra, including but not limited tohCAP-18/LL-37, CRAMP, Bac4, OaBac5; prophenin-1, protegrin-1, or PR-39;a molecule that executes, stimulates, or inhibits chemokine-related orthrombocidin-related responses, as described supra, including but notlimited to CC chemokines, CXC chemokines, C chemokines, CX3C chemokines,CC chemokine receptors, CXC chemokine receptors, C chemokine receptors,CX3C chemokine receptors, JAK proteins, STAT proteins, fibrinopeptide A,fibrinopeptide B, or thymosin beta 4; a molecule that executes,stimulates, or inhibits interferon-related or cytokine-relatedresponses, as described supra (including but not limited tointerferon-alpha (Homo sapiens, #NM_(—)002169, NM_(—)021002, J00207; Musmusculus, #NM_(—)010502, NM_(—)010503, NM_(—)010507, NM_(—)008333,M68944, M13710); interferon-beta (Homo sapiens, #M25460, NM_(—)002176;Mus musculus, #NM_(—)010510); interferon-gamma (Homo sapiens,#NM_(—)000619, J00219; Mus musculus, #M28621); interferon-delta;interferon-tau; interferon-omega (Homo sapiens, #NM_(—)002177);interleukin 1 (IL-1: Homo sapiens, #NM_(—)000575, NM_(—)012275,NM_(—)019618, NM_(—)000576, NM_(—)014439; Mus musculus, #NM_(—)019450,NM_(—)019451, AF230378); interleukin 2 (IL-2: Homo sapiens,#NM_(—)000586); interleukin 3 (IL-3: Homo sapiens, #NM_(—)000588; Musmusculus, #A02046); interleukin 4 (IL-4: Homo sapiens, #NM_(—)000589,NM_(—)172348; Mus musculus, #NM_(—)021283); interleukin 5 (IL-5: Homosapiens, #NM_(—)000879; Mus musculus, #NM_(—)010558); interleukin 6(IL-6: Homo sapiens, #NM_(—)000600; Mus musculus, #NM_(—)031168);interleukin 7 (IL-7: Homo sapiens, #NM_(—)000880, AH006906; Musmusculus, #NM_(—)008371); interleukin 9 (IL-9: Homo sapiens,#NM_(—)000590); interleukin 12 (IL-12: Homo sapiens, #NM_(—)000882,NM_(—)002187; Mus musculus, #NM_(—)008351, NM_(—)008352); interleukin 15(IL-15: Homo sapiens, #NM_(—)172174, NM_(—)172175, NM_(—)000585; Musmusculus, #NM_(—)008357); cytokine receptors and related signalingmolecules (W. E. Paul (ed.), Fundamental Immunology (4th ed.,Lippincott-Raven, Philadelphia, 1999), Chapters 21 and 22); interferontype I receptor subunit 1 (IFNAR1: Homo sapiens, #NM_(—)000629; Musmusculus, #NM_(—)010508); interferon type I receptor subunit 2 (IFNAR2:Homo sapiens, #NM_(—)000874; Mus musculus, #NM_(—)010509); janus kinase1 (JAK1: Homo sapiens, #NP_(—)002218; Mus musculus, #NP_(—)666257);janus kinase 2 (JAK2: Homo sapiens, #AAC23653, AAC23982, NP_(—)004963;Mus musculus, #NP_(—)032439, AAN62560); JAK3; Tyk2; signal transducerand activator of transcription 1 (STAT1: Homo sapiens, #NM_(—)007315,NM_(—)139266; Mus musculus, #U06924); signal transducer and activator oftranscription 2 (STAT2: Homo sapiens, #NM_(—)005419; Mus musculus,AF206162); STAT3; STAT4; STAT5; STAT6; interferon-stimulated gene factor3 gamma (ISGF3 gamma: Homo sapiens, #Q00978, NM_(—)006084; Mus musculus,#NM_(—)008394) interferon regulatory factor 1 (IRF1: Homo sapiens,#NM_(—)002198, P10914; Mus musculus, #NM_(—)008390); interferonregulatory factor 3 (IRF3: Homo sapiens, #NM_(—)001571, Z56281; Musmusculus, #NM_(—)016849, U75839, U75840); interferon regulatory factor 5(IRF5: Homo sapiens, #Q13568, U51127; Mus musculus, #AAB81997,NP_(—)036187); interferon regulatory factor 6 (IRF6: Homo sapiens,#AF027292, NM_(—)006147; Mus musculus, #U73029); interferon regulatoryfactor 7 (IRF7: Homo sapiens, #U53830, U53831, U53832, AF076494, U73036;Mus musculus, #NM_(—)016850, U73037); interferon regulatory factor 8(IRF8); a constitutively active interferon regulatory factor; proteinkinase R (PKR: Homo sapiens, #AAC50768; Mus musculus, #Q03963; S.Nanduri et al. (1998) EMBO J. 17, 5458-5465); constitutively active PKR;2′,5′-oligoadenylate synthetases (Homo sapiens forms including #P00973,P29728, AAD28543; Mus musculus forms including P11928; S. Y. Desai etal. (1995) J. Biol. Chem. 270, 3454-3461); constitutively active2′,5′-oligoadenylate synthetases; RNase L (Homo sapiens, #CAA52920);constitutively active RNase L; promyelocytic leukemia protein (PML: W.V. Bonilla et al. (2002) Journal of Virology 76, 3810-3818); p56 orrelated proteins (J. Guo et al. (2000) EMBO Journal 19, 6891-6899; G. C.Sen (2000) Seminars in Cancer Biology 10, 93-101); p200 or relatedproteins (G. C. Sen (2000) Seminars in Cancer Biology 10, 93-101); ADAR1(Homo sapiens, #U18121; Mus musculus, #NP_(—)062629); Mx1 (Homo sapiens,#NM_(—)002462); or Mx2 (Homo sapiens, #NM_(—)002463)); a molecule thatinhibits budding or release of pathogens from an infected cell, asdescribed supra (including but not limited to Hrs, particularly whenoverexpressed (N. Bishop et al. (2002) Journal of Cell Biology 157,91-101; L. Chin et al. (2001) Journal of Biological Chemistry 276,7069-7078; C. Raiborg et al. (2002) Nature Cell Biology 4, 394-398);defective Vps4 mutants such as K173Q or E228Q, particularly whenoverexpressed (J. E. Garrus et al. (2001) Cell 107, 55-65); smallinterfering RNA that inhibits Tsg101 expression (N. Bishop et al. (2002)Journal of Cell Biology 157, 91-101; J. E. Garrus et al. (2001) Cell107, 55-65); truncated AP-50 consisting of approximately amino acids121-435, or other defective mutant of AP-50, particularly whenoverexpressed (B. A. Puffer et al. (1998) Journal of Virology 72,10218-10221); WW-domain-containing fragment of LDI-1, Nedd4,Yes-associated protein, KIAA0439 gene product, or other defectiveNedd4-related proteins, particularly when overexpressed (A. Kikonyogo etal. (2001) Proc. Natl. Acad. Sci. USA 98, 11199-11204; A. Patnaik and J.W. Wills (2002) Journal of Virology 76, 2789-2795); a peptide consistingof the HIV p6 Gag PTAPP-motif-containing late (L) domain (L. VerPlank etal. (2001) Proc. Natl. Acad. Sci. USA 98, 7724-7729) or other viral late(L) domain containing PTAP, PSAP, PPXY, YPDL, or YXXL motifs (J.Martin-Serrano et al. (2001) Nature Medicine 7, 1313-1319; A. Patnaikand J. W. Wills (2002) Journal of Virology 76, 2789-2795); amino acids1-167 of Tsg101, TSG-5′ fragment of Tsg101, or similar amino-terminalfragment of Tsg101, particularly when overexpressed (D. G. Demirov etal. (2002) Proc. Natl. Acad. Sci. USA 99, 955-9601; E. L. Myers and J.F. Allen (2002) Journal of Virology 76, 11226-11235); a mutant of Tsg101(M. Babst et al. (2000) Traffic 1, 248-258; L. VerPlank et al. (2001)Proc. Natl. Acad. Sci. USA 98, 7724-7729; J. Martin-Serrano et al.(2001) Nature Medicine 7, 1313-1319; O. Pornillos et al. (2002) EMBOJournal 21, 2397-2406) with reduced capacity to aid viral budding; acasein kinase 2 (CK2) inhibitor, such as the peptide RRADDSDDDDD (SEQ IDNO: 472) (E. K. Hui and D. P. Nayak (2002) Journal of General Virology83, 3055-3066); or G protein signalling inhibitors (E. K. Hui and D. P.Nayak (2002) Journal of General Virology 83, 3055-3066); a molecule thatbinds to a cellular or pathogen molecule (for example to one or more ofthe following molecules: Tsg101, Vps4, casein kinase 2, Hrs, hVps28,Eap30, Eap20, Eap45, Chmp1, Chmp2, Chmp3, Chmp4, Chmp5, Chmp6, AP-50,Nedd4-related proteins, WW-domain-containing proteins, orL-domain-containing proteins; O. Pornillos et al. (2002) TRENDS in CellBiology 12, 569-579; P. Gomez-Puertas et al. (2000) Journal of Virology74, 11538-11547; E. Katz et al. (2002) Journal of Virology 76,11637-11644) that is involved in budding or release of pathogens from aninfected cell); a molecule that executes or stimulates apoptosis-relatedor other cell-death-related responses, as described supra (including butnot limited to p53 (Homo sapiens, #AAF36354 through AAF36382; Musmusculus, #AAC05704, AAD39535, AAF43275, AAF43276, AAK53397); Bax (Homosapiens, #NM_(—)004324); Bid (Homo sapiens, #NM_(—)001196); apoptoticprotease activating factor 1 (Apaf-1: Homo sapiens, #NM_(—)013229,NM_(—)001160; Mus musculus, #NP_(—)033814); Fas/CD95 (Homo sapiens,#AAC16236, AAC16237; Mus musculus, #AAG02410); TNF receptors (Homosapiens, #NP_(—)001056; V. Baud and M. Karin (2001) TRENDS in CellBiology 11, 372-377; U. Sartorius et al. (2001) Chembiochem 2, 20-29);FLICE-activated death domain (FADD: Homo sapiens, #U24231; Mus musculus,#NM_(—)010175); TRADD (Homo sapiens, #NP_(—)003780, CAC38018); granzymeB (Homo sapiens, #AAH30195, NP_(—)004122; Mus musculus, #AAH02085,NP_(—)038570); constitutively active granzyme B; Smac/DIABLO (Homosapiens, #NM_(—)019887); caspases (including but not restricted toCaspase 1, Homo sapiens, #NM_(—)001223; Caspase 2, Homo sapiens,#NM_(—)032982, NM 001224, NM_(—)032983, and NM_(—)032984; Caspase 3,Homo sapiens, #U26943; Caspase 4, Homo sapiens, #AAH17839; Caspase 5,Homo sapiens, #NP_(—)004338; Caspase 6, Homo sapiens, #NM_(—)001226 andNM_(—)032992; Caspase 7, Homo sapiens, #XM_(—)053352; Caspase 8, Homosapiens, #NM_(—)001228; Caspase 9, Homo sapiens, #AB019197; Caspase 10,Homo sapiens, #XP_(—)027991; Caspase 13, Homo sapiens, #AAC28380;Caspase 14, Homo sapiens, #NP_(—)036246; Caspase 1, Mus musculus,#BC008152; Caspase 2, Mus musculus, #NM_(—)007610; Caspase 3, Musmusculus, #NM_(—)009810; Caspase 6, Mus musculus, #BC002022; Caspase 7,Mus musculus, #BC005428; Caspase 8, Mus musculus, #BC006737; Caspase 9,Mus musculus, #NM_(—)015733; Caspase 11, Mus musculus, #NM_(—)007609;Caspase 12, Mus musculus, #NM_(—)009808; Caspase 14, Mus musculus,#AF092997; and CED-3 caspase, Caenorhabditis elegans, #AF210702); aconstitutively active caspase; calpains (T. Lu et al., (2002) Biochimicaet Biophysica Acta 1590, 16-26)); a molecule that degrades components ofcells or pathogens, as described supra (for example: proteases,including but not limited to chymotrypsin, trypsin, or elastase; DNases,including but not limited to caspase-activated DNase (CAD),constitutively active CAD (N. Inohara et al. (1999) Journal ofBiological Chemistry 274, 270-274), or restriction enzymes; RNases,including but not limited to RNase III (Homo sapiens, #AF189011;Escherichia coli, #NP_(—)417062, NC_(—)000913), RNt1p (Saccharomycescerevisiae, #U27016), Pac1, (Schizosaccharomyces pombe, #X54998), RNaseA, or RNase L; glycosidases, including but not limited to N-glycanase,endoglycosidase H, O-glycanase, endoglycosidase F2, sialidase, orbeta-galactosidase; or lipases, including but not limited tophospholipase A1, phospholipase A2, phospholipase C, or phospholipaseD); a molecule that is toxic to an infected host cell or a pathogencell, as described supra (including but not limited to an intracellularbacterial toxin (B. B. Finlay and P. Cossart (1997) Science 276,718-725; C. Montecucco et al. (1994) FEBS Lett. 346, 92-98; P. O. Falneset al. (2001) Biochemistry 40, 4349-4358) that has been modified so thatit cannot cross cellular plasma membranes (as will be understood by oneof skill in the art), such as the A (21 kDa) fragment of diptheriatoxin; a molecule that is toxic to a pathogen cell, including but notlimited to penicillin, erythromycin, tetracycline, rifampin,amphotericin B, metronidazole, or mefloquine; an ATP inhibitor (E. K.Hui and D. P. Nayak (2001) Virology 290, 329-341); or a toxin thatinhibits transcription, translation, replication, oxidativephosphorylation, cytoskeletal processes, or other cell and/or pathogenfunctions).

Also included in this invention are chimeric transcriptions factors. Theheat shock element (HSE) binding domain is approximately amino acids13-121 of human heat shock factor 1 (HSF1) (M. Green et al. (1995)Molecular and Cellular Biology 15, 3354-3362; S.-G. Ahn et al. (2001)Genes & Development 15, 2134-2145). One or more copies of this domaincan be isolated and linked together, preferably by flexible hydrophilicamino acid sequences in a chimeric transcription factor. In a preferredembodiment, three copies of the HSF1 DNA binding domain, preferablyseparated by flexible hydrophilic amino acid sequences are present inthe chimeric transcription factor.

Interferon-stimulated gene factor 3 gamma (ISGF-3 gamma) inducestranscription in response to type-I interferon. The ISGF-3 gamma DNAbinding domain is approximately amino acids 1-112. (NCBI Accession#Q00978; H. A. R. Bluyssen, J. E. Durbin, and D. E. Levy (1996) Cytokine& Growth Factor Reviews 7, 11-17; Y. Mamane et al. (1999) Gene 237,1-14). The ISGF-3 gamma DNA binding domain can be isolated and used in agenetically-engineered chimeric transcription factor, as describedbelow.

Interferon regulatory factor 3 (IRF-3) induces transcription in responseto dsRNA. Excluding regions needed for regulation of its activation, theDNA binding domain of IRF-3 is approximately amino acids 1-97 (Y. Mamaneet al. (1999) Gene 237, 1-14; R. Lin, Y. Mamane, and J. Hiscott (1999)Molecular and Cellular Biology 19, 2465-2474). The DNA binding domain ofIRF-3 can also be isolated and used in a genetically-engineered chimerictranscription factor, as described below.

Interferon regulatory factor 1 (IRF-1) upregulates expression of MHCClass I and functions in other ways to improve immune and antiviralresponses. The IRF-1 DNA binding domain is approximately amino acids1-109 (NCBI Accession # P10914, NP_(—)002189; C. E. Samuel (2001)Clinical Microbiology Reviews 14, 778-809; S. J. P. Gobin et al. (1999)J Immunology 163, 1428-1434; W.-C. Au et al. (1995) Proc. Natl. Acad.Sci. 92, 11657-11661; S. Kirchhoff et al. (2000) Eur. J. Biochem. 267,6753-6761; Y. Mamane et al. (1999) Gene 237, 1-14). The IRF-1 DNAbinding domain can also be isolated and used in a genetically-engineeredchimeric transcription factor, as described below.

p53 upregulates apoptosis-related and other genes when activated. Thep53 DNA binding domain is approximately amino acids 100-300. (A. Ayed etal. (2001) Nature Structural Biology 8, 756-760; B. F. Mueller-Tiemannet al. (1998) Proc. Natl. Acad. Sci. 95, 6079-6084; M. E. Anderson etal. (1997) Molecular and Cellular Biology 17, 6255-6264; Y. Wang et al.(1995) Molecular and Cellular Biology 15, 2157-2165). In a preferredembodiment, the chimeric transcription factor has four copies of the p53DNA binding domain, preferably separated by flexible hydrophilic aminoacid sequences. The p53 DNA binding domain can be isolated and used in agenetically-engineered chimeric transcription factor, as describedbelow.

XBP1 (K. Lee et al. (2002) Genes & Development 16, 452-466; H. Yoshidaet al. (2001) Cell 107, 881-891) and ATF6 (X. Chen et al. (2002) Journalof Biological Chemistry 277, 13045-13052; J. Shi et al. (2002)Developmental Cell 3, 99-111; Y. Wang et al. (2000) Journal ofBiological Chemistry 275, 27013-27020) upregulateunfolded-protein-response orendoplasmic-reticulum-associated-protein-degradation-response genes.

CIITA (M. W. Linhoff et al. (2001) Molecular and Cellular Biology 21,3001-3011; A. Muhlethaler-Mottet et al. (1997) EMBO Journal 16,2851-2860) upregulates MHC Class II genes when activated. The CARDand/or acidic domains of CIITA isoforms act as transcriptionalactivators.

NF kappa B upregulates inflammatory-response genes when activated (F. E.Chen and G. Ghosh (1999) Oncogene 18, 6845-6852; H. L. Pahl (1999)Oncogene 18, 6853-6866).

In one embodiment, a chimeric molecule or agent of the inventionincludes a chimeric transcription factor in which the naturalDNA-binding domain of ISGF-3 gamma is replaced with one or more of thefollowing: one or more DNA-binding domains isolated from XBP1; one ormore DNA-binding domains isolated from ATF6; one or more transcriptionactivation domains isolated from CIITA; one or more HSE-binding domains;one or more DNA-binding domains isolated from NF kappa B; one or moreDNA-binding domains isolated from IRF-1.

In another embodiment, a chimeric molecule or agent of the inventionincludes a chimeric transcription factor in which the naturalDNA-binding domain (approximately amino acids 1-97) of IRF-3 is replacedwith one or more of the following: one or more DNA-binding domainsisolated from XBP1; one or more DNA-binding domains isolated from ATF6;one or more transcription activation domains isolated from CIITA; one ormore DNA-binding domains isolated from ISGF-3 gamma; one or moreDNA-binding domains isolated from p53; one or more HSE-binding domains;one or more DNA-binding domains isolated from NF kappa B; one or moreDNA-binding domains isolated from IRF-1.

In another embodiment, a chimeric molecule or agent of the inventionincludes a chimeric transcription factor in which the naturalDNA-binding domains of NF kappa B are replaced with one or more of thefollowing: one or more DNA-binding domains isolated from XBP1; one ormore DNA-binding domains isolated from ATF6; one or more transcriptionactivation domains isolated from CIITA; one or more DNA-binding domainsisolated from ISGF-3 gamma; one or more DNA-binding domains isolatedfrom IRF-3; one or more HSE-binding domains; one or more DNA-bindingdomains isolated from IRF-1.

In another embodiment, a chimeric molecule or agent of the inventionincludes a chimeric transcription factor in which the naturalDNA-binding domain of ATF6 is replaced with one or more of thefollowing: one or more DNA-binding domains isolated from XBP1; one ormore DNA-binding domains isolated from p53; one or more transcriptionactivation domains isolated from CIITA; one or more DNA-binding domainsisolated from ISGF-3 gamma; one or more DNA-binding domains isolatedfrom IRF-3; one or more HSE-binding domains; one or more DNA-bindingdomains isolated from NF kappa B; one or more DNA-binding domainsisolated from IRF-1.

In another embodiment, a chimeric molecule or agent of the inventionincludes a chimeric transcription factor in which the naturalDNA-binding domain of p53 is replaced with one or more of the following:one or more DNA-binding domains isolated from XBP1; one or moreDNA-binding domains isolated from ATF6; one or more transcriptionactivation domains isolated from CIITA; one or more DNA-binding domainsisolated from ISGF-3 gamma; one or more DNA-binding domains isolatedfrom IRF-3; one or more HSE-binding domains; one or more DNA-bindingdomains isolated from NF kappa B; one or more DNA-binding domainsisolated from IRF-1.

In another embodiment, a chimeric molecule or agent of the inventionincludes a chimeric transcription factor in which the naturaltranscription activation domain of CIITA (the CARD and/or acidic domain)is replaced with one or more of the following: one or more DNA-bindingdomains isolated from XBP1; one or more DNA-binding domains isolatedfrom ATF6; one or more DNA-binding domains isolated from ISGF-3 gamma;one or more DNA-binding domains isolated from IRF-3; one or moreDNA-binding domains isolated from p53; one or more HSE-binding domains;one or more DNA-binding domains isolated from NF kappa B; one or moreDNA-binding domains isolated from IRF-1.

In another embodiment, a chimeric molecule or agent of the inventionincludes a chimeric transcription factor in which the naturalDNA-binding domain of IRF-1 is replaced with one or more of thefollowing: one or more DNA-binding domains isolated from XBP1; one ormore DNA-binding domains isolated from ATF6; one or more transcriptionactivation domains isolated from CIITA; one or more DNA-binding domainsisolated from ISGF-3 gamma; one or more HSE-binding domains; one or moreDNA-binding domains isolated from NF kappa B.

In another embodiment, a chimeric molecule or agent of the inventionincludes a chimeric transcription factor in which the naturalDNA-binding domain (approximately amino acids 13-121) of HSF1 isreplaced with one or more of the following: one or more DNA-bindingdomains isolated from XBP1; one or more DNA-binding domains isolatedfrom ATF6; one or more transcription activation domains isolated fromCIITA; one or more DNA-binding domains isolated from ISGF-3 gamma; oneor more DNA-binding domains isolated from IRF-3; one or more HSE-bindingdomains; one or more DNA-binding domains isolated from NF kappa B; oneor more DNA-binding domains isolated from IRF-1.

An agent of the invention, as described herein, can comprise at leastone pathogen-interacting molecular structure and at least oneeffector-mediating molecular structure. Alternatively, an agent of theinvention can comprise at least one pathogen-induced product-interactingmolecular structure and at least one effector-mediating molecularstructure.

A pathogen-interacting molecular structure, as used herein, is generallydirected to an isolated molecular structure that is capable ofrecognizing or binding (interacting with) a pathogen, pathogen componentor pathogen product. The term pathogen-interacting molecular structureis structure of a molecule that includes at least the minimal regionnecessary to perform the function of interacting with a pathogen,pathogen component or pathogen product. Isolated pathogen-interactingmolecular structures, as used herein, encompass the pathogen-detectiondomains described supra. Furthermore, a pathogen-interacting molecularstructure can be more than or less than a domain of the describedproteins or polynucleotide sequences, but still retains the function ofinteracting with a pathogen, pathogen component or pathogen product.

A pathogen-induced product-interacting molecular structure, as usedherein, is generally directed to an isolated molecular structure that iscapable of recognizing or binding (interacting with) a pathogen-inducedproduct, as described herein and include, for example and withoutlimitation, cytokines such as an interferons or interleukins,unfolded-protein response or endoplasmic reticulum-associated proteindegradation response signaling molecules, stress response orinflammatory response signaling molecules, 2′,5′-oligoadenylate, andapoptosis signaling molecules. The term pathogen-inducedproduct-interacting molecular structure is the structure of a moleculethat includes at least the minimal region necessary to perform thefunction of interacting with a pathogen-induced product. Isolatedpathogen-induced product-interacting molecular structures, as usedherein, encompass the pathogen-induced product-detection domainsdescribed supra. Furthermore, a pathogen-induced product-interactingmolecular structure can be more than or less than a domain of thedescribed proteins or polynucleotide sequences, but retains the functionof interacting with a pathogen-induced product.

The effector-mediating molecular structure, as used herein, is generallydirected to an isolated molecular structure that is capable of mediatinga wide range of effector functions, as described supra for an effectordomain of a chimeric molecule of the invention. In particular, theeffector-mediating molecular structure of this invention can mediate thesame responses as an effector domain, for example and withoutlimitation: (1) an interferon response; (2) an apoptosis response; (3) astress response; (4) an inflammatory response; (5) an enhanced immuneresponse; (6) a degradative response; (7) inhibition of transportbetween the cytoplasm and the nucleus of a cell; (8) an unfolded-proteinresponse or endoplasmic reticulum-associated protein degradationresponse; or (9) alteration of the endocytic or phagocytic pathway, allof which are discussed supra.

The molecular structures of the described agent can be isolated fromnaturally-occurring molecules, such as a cellular protein, that normallyrecognize a pathogen, pathogen component, pathogen product, orpathogen-induced product, or is a mediator of a wide range of effectorfunction. Molecular structures can be isolated from a wide range ofknown cellular proteins from a number of different organisms, includingfor example, humans, non-human primates, rodents, plants, Drosophila,yeast, bacteria and the like, as will be appreciated by one of skill inthe art. The molecular structures can also be synthetically-derived,such as by chemically modifying a naturally-occurring molecule, orotherwise manipulating a naturally-occurring molecule to enhance,optimize, or modify the molecular structures, using standard techniquesknown to those of skill in the art, or alternatively, they can be asynthetic product such as a small molecule or a peptidomimetic.Furthermore, the molecular structures of the agent can be an antibody(including, for example, antibody fragments, such as Fab, Fab′, F(ab′)₂,and fragments including either a V_(L) or V_(H) domain, single chainantibodies, bi-specific, chimeric or humanized antibodies), thatperforms the function of the molecular structure.

More than one detection and/or effector domain can be present in achimeric molecule. These can be the same or different domains.Similarly, more than one detection and/or effector molecular structurescan be present in an agent of the invention.

A chimeric molecule or agent of the invention can be a nonnaturallyoccurring molecule that contains two or more binding sites for apathogen or pathogen product. The two or more binding sites promoteagglomeration of pathogens or pathogen products and thereby directly orindirectly promote an anti-pathogen effect. For example, a chimericmolecule or agent of the invention can have two or more binding sitesfor LPS (for example, sites that mimic the LPS-binding domain fromapproximately amino acids 1-199 of human BPI or other LPS-bindingdomains as described supra); two or more binding sites for peptidoglycan(for example, sites that mimic the peptidoglycan-binding domain from theextracellular domain of human TLR2); two or more binding sites formuramyl dipeptide (for example, sites that mimic themuramyl-dipeptide-binding domain from approximately amino acids 744-1040of human Nod2); two or more binding sites for bacterial flagellin (forexample, sites that mimic the flagellin-binding domain from theextracellular domain of human TLR5); two or more binding sites forbacterial type III secretion systems; two or more binding sites for CpGDNA (for example, sites that mimic the CpG-DNA-binding domain from theextracellular domain of human TLR9); two or more binding sites forzymosan (for example, sites that mimic the zymosan-binding domain fromthe extracellular domain of human TLR2); two or more binding sites for apathogenic form of a prion (for example, sites that mimic a portion of anonpathogenic prion form that binds to a pathogenic prion form (such asapproximately amino acids 119-136 of hamster prion protein; J. Chabry etal. (1999) Journal of Virology 73, 6245-6250)); two or more bindingsites for dsRNA (for example, sites that contain lividomycin or thatmimic the dsRNA-binding domain of lividomycin, protein kinase R, orother dsRNA-binding domains as described supra); two or more bindingsites for viral late domains (for example and without restriction, sitesthat bind to viral late domain motifs such as PTAP, PSAP, PPXY, YPDL, orYXXL, as described supra); two or more binding sites for viralglycoproteins (for example and without restriction, sites that mimic thehemagglutinin-binding domain of human NK cell activation receptorNKp46).

The chimeric molecules and agents as described herein can be assembledor joined between the domains or molecular structures by, for example,peptide linkage, covalent bonding, artificial linkage, or a flexiblelinker region normally associated with either domain or molecularstructure.

Alternatively, the domains of the chimeric molecules or molecularstructures of the agent can be separated. Separate domains or molecularstructures are capable of being assembled or joined through severalmechanisms, for example and without limitation, through the interactionwith another reagent, for example a bi-specific antibody, a chemicalcross-linker, or other methods as will be appreciated by one of skill inthe art. The separate domains can also be assembled together vianon-covalent bonds, such as through electrostatic interactions and thelike. Furthermore, the separate domains or molecular structures canmediate their effects either directly or indirectly through such agentsas secondary signaling molecules, as will be understood by one of skillin the art.

Attached to the separate domains or separate molecular structures can befurther domains or structures that can mediate the joining of theseparate domains or structures to form the chimeric molecule or agent,for example, one domain or molecular structure can have one or morestreptavidin molecules attached, and the other domain or molecularstructure can have one or more biotin molecules attached, thus thespecific biotin-streptavidin interaction mediates the forming of achimeric molecule or agent. Other suitable interaction domains orstructures will be recognized by one of skill in the art.

The chimeric molecule or agent can additionally contain cellulartargeting tags. For example, tags that direct the chimeric molecule oragent to the cell membrane or cellular organelles, the nucleus, or othervarieties of tags. Such tags can be used to mediate crossing of themembrane by the chimeric molecule or agent. Suitable protein uptake tagsinclude, for example and without limitation: (1) poly-arginine andrelated peptoid tags (L. Chen et al. (2001) Chem. Biol. 8: 1123-1129, P.A. Wender et al. (2000) Proc. Natl. Acad. Sci. 97: 13003-13008); (2) HIVTAT protein, its Protein Transduction Domain (PTD) spanningapproximately amino acids 47-57, or synthetic analogs of the PTD (M.Becker-Hapak, S. S. McAllister, and S. F. Dowdy (2001) Methods 24:247-256, A. Ho et al. (2001) Cancer Res. 61: 474-477); (3) DrosophilaAntennapedia protein, the domain spanning approximately amino acids43-58 also called Helix-3 or Penetratin-1, or synthetic analogs thereof(D. Derossi, G. Chassaing, and A. Prochiantz (1998) Trends Cell Biol. 8:84-87, A. Prochiantz (1996) Curr. Opin. Neurobiol. 6: 629-63); (4)Herpesvirus VP22 protein, the domain spanning approximately amino acids159-301, or portions or synthetic analogs thereof (N. Normand, H. vanLeeuwen, and P. O'Hare (2001) J. Biol. Chem. 276: 15042-15050, A.Phelan, G. Elliott, and P. O'Hare (1998) Nat. Biotech. 16: 440-443); (5)Membrane-Translocating Sequence (MTS) from Kaposi fibroblast growthfactor or related amino acid sequences such as AAVLLPVLLAAP (SEQ ID NO:473) (M. Rojas, J. P. Donahue, Z. Tan, and Y.-Z. Lin (1998) Nat.Biotech. 16: 370-375, C. Du, S. Yao, M. Rojas, and Y.-Z. Lin (1998) J.Peptide Res. 51: 235-243); (6) Pep-1, MPG, and similar peptides (M. C.Morris et al. (2001) Nat. Biotech. 19: 1173-1176, M. C. Morris et al.(1999) Nuc. Ac. Res. 27: 3510-3517); (7) Transportan, Transportan 2, andsimilar peptides (M. Pooga et al. (1998) FASEB J. 12: 67-77; M. Pooga etal. (1998) Ann. New York Acad. Sci. 863: 450-453); (8) Amphipathic modelpeptide and related peptide sequences (A. Scheller et al. (2000) Eur. J.Biochem. 267: 6043-6049, A. Scheller et al. (1999) J. Pept. Sci. 5:185-194); (9) Tag protein to be delivered with approximately amino acids1-254 of Bacillus anthracis lethal factor (LF), and administer alongwith B. anthracis protective antigen (PA) to deliver the tagged proteininto cells, or similar methods (S. H. Leppla, N. Arora, and M. Varughese(1999) J. App. Micro. 87: 284, T. J. Goletz et al. (1997) Proc. Natl.Acad. Sci. 94: 12059-12064); and (10) Folic acid (C. P. Leamon and P. S.Low (2001) Drug Discov. Today 6: 44-51, C. P. Leamon, R. B. DePrince,and R. W. Hendren (1999) J. Drug Targeting 7: 157-169). Methods forattaching uptake tags to the proteins employ standard methods and willbe recognized by one of skill in the art.

Optionally the chimeric molecule or agent can include one or morebinding sites for one or more natural inhibitory or regulatory moleculesin order to facilitate the inhibitory or regulatory molecule(s) toregulate the activity of the chimeric molecule or agent, and preventtoxicity in uninfected cells. For example and without restriction, thechimeric molecule or agent can include one or more binding sites for oneof more of the following: the natural P58 inhibitor of protein kinase Rand PERK (W. Yan et al. (2002) Proc. Natl. Acad. Sci. USA 99,15920-15925); the natural RLI inhibitor of RNase L (C. Bisbal et al.(1995) Journal of Biological Chemistry 270, 13308-13317); the naturalXIAP inhibitor of caspase 9 (S. M. Srinivasula et al. (2001) Nature 410,112-116); or the natural HSBP1 inhibitor of HSF1 (R. I. Morimoto (1998)Genes & Development 12, 3788-3796).

The chimeric molecule and its individual domains, and the agent and itsindividual molecular structures, can be of a variety of compounds orsubstances, for example, protein, DNA, RNA, single chain antibodies,small molecule drugs, pro-drugs, or peptidomimetics. A DNA or RNAencoding a molecule of interest can, optionally, be operatively-linkedto a promoter. Furthermore, said promoter can be conditionallyregulated.

The chimeric molecule or agent can be administered to a cell or organismbefore (prophylactically) or after infection (therapeutically).

The composition of the present invention can be administered by anyknown route of administration. For example, the route of administrationcan be intravenous, intramuscular, intraarterial, intraperitoneal,intrasternal, subcutaneous, intraocular, inhalation, orally and byintraarticular injection or infusion.

The composition of the present invention can be, for example, solid (orsemi-solid, such as, creams or a gelatin-type substance), liquid, oraerosol. Examples of solid compositions include pills, creams, andimplantable dosage units. The pills can be administered orally, thecreams can be administered topically. The implantable dosage unit can beadministered locally, or implanted for systemic release of the chimericmolecules or agents, for example subcutaneously. Examples of liquidcomposition include formulations adapted for injection subcutaneously,intravenously, intraarterially, and formulations for topical andadministration. Examples of aersol formulation include inhalerformulation for administration to the lungs.

Pharmaceutical compositions for parenteral injection comprisepharmaceutically acceptable sterile aqueous or nonaqueous solutions,dispersions, suspensions or emulsions, as well as sterile powders forreconstitution into sterile injectable solutions, or dispersions, justprior to use. Examples of suitable aqueous and nonaqueous carriers,diluents, solvents or vehicles include water, ethanol, polyols (e.g.,glycerol, propylene glycol, polyethylene glycol and the like),carboxymethylcellulose and suitable mixtures thereof, vegetable oils(e.g., olive oil) and injectable organic esters such as ethyl oleate.Proper fluidity can be maintained, for example, by the use of coatingmaterials such as lecithin, by the maintenance of the required particlesize in the case of dispersions and by the use of surfactants. Thesecompositions can also contain adjuvants such as preservatives, wettingagents, emulsifying agents and dispersing agents. Prevention of theaction of microorganisms may be ensured by the inclusion of variousantibacterial and antifungal agents such as paraben, chlorobutanol,phenol sorbic acid and the like. It can also be desirable to includeisotonic agents such as sugars, sodium chloride and the like. Prolongedabsorption of the injectable pharmaceutical form can be brought about bythe inclusion of agents, such as aluminum monostearate and gelatin,which delay absorption. Injectable depot forms are made by formingmicroencapsule matrices of the drug in biodegradable polymers such aspolylactide-polyglycolide, poly(orthoesters) and poly(anhydrides).Depending upon the ratio of drug to polymer and the nature of theparticular polmer employed, the rate of drug release can be controlled.Depot injectable formulations are also prepared by entrapping the drugin liposomes or microemulsions which are compatible with body tissues.The injectable formulations can be sterilized, for example, byfiltration through a bacterial-retaining filter or by incorporatingsterilizing agents in the form of sterile solid compositions which canbe dissolved or dispersed in sterile water or other sterile injectablemedia just prior to use.

The compositions of the present invention can includepharmaceutically-acceptable salts of the compositions described herein,e.g., which can be derived from inorganic or organic acids. A“pharmaceutically-acceptable salt” is meant to describe those saltswhich are, within the scope of sound medical judgement, suitable for usein contact with the tissues of animals, preferably mammals, withoutundue toxicity, irritation, allergic response and the like and arecommensurate with a reasonable benefit/risk ratio. Pharmaceuticallyacceptable salts are well-known in the art. For example, S. M. Berge, etal. describe pharmaceutically acceptable salts in detail in J.Pharmaceutical Sciences (1977) 66:1 et seq. Pharmaceutically acceptablesalts include the acid addition salts (formed with the free amino groupsof the polypeptide) that are formed with inorganic acids such as, forexample, hydrochloric or phosphoric acids, or such organic acids asacetic, tartaric, mandelic and the like. Salts formed with the freecarboxyl groups can also be derived from inorganic bases such as, forexample, sodium, potassium, ammonium, calcium or ferric hydroxides, andsuch organic bases as isopropylamine, trimethylamine, 2-ethylaminoethanol, histidine, procaine and the like. The salts can be prepared insitu during the final isolation and purification of the compounds of theinvention or separately by reacting a free base function with a suitableorganic acid. Representative acid addition salts include, but are notlimited to acetate, adipate, alginate, citrate, aspartate, benzoate,benzenesulfonate, bisulfate, butyrate, camphorate, camphorsufonate,digluconate, glycerophosphate, hemisulfate, heptonoate, hexanoate,fumarate, hydrochloride, hydrobromide, hydroiodide,2-hydroxymethanesulfonate (isethionate), lactate, maleate,methanesulfonate, nicotinate, 2-naphthalenesulfonate, oxalate, pamoate,pectinate, persulfate, 3-phenylpropionate, picrate, pivalate,propionate, succinate, tartate, thiocyanate, phosphate, glutamate,bicarbonate, p-toluenesulfonate and undecanoate. Also, the basicnitrogen-containing groups can be quaternized with such agents as loweralkyl halides such as methyl, ethyl, propyl, and butyl chlorides,bromides and iodides; dialkyl sulfates like dimethyl, diethyl, dibutyl,and diamyl sulfates; long chain halides such as decyl, lauryl, myristyland stearyl chlorides, bromides and iodides; arylalkyl halides likebenzyl and phenethyl bromides and others. Water or oil-soluble ordispersible products are thereby obtained. Examples of acids which canbe employed to form pharmaceutically acceptable acid addition saltsinclude such inorganic acids as hydrochloric acid, hydrobromic acid,sulphuric acid and phosphoric acid and such organic acids as oxalicacid, maleic acid, succinic acid and citric acid.

As used herein, the terms “pharmaceutically acceptable,”“physiologically tolerable” and grammatical variations thereof as theyrefer to compositions, carriers, diluents and reagents, are usedinterchangeably and represent materials that are capable ofadministration to or upon an animal, preferably a mammal, with a minimumof undesirable physiological effects such as nausea, dizziness, gastricupset and the like. The preparation of a pharmacological compositionthat contains active ingredients dissolved or dispersed therein is wellunderstood in the art and need not be limited based on formulation.Typically such compositions are prepared as injectables either as liquidsolutions or suspensions, however, solid forms suitable for solution, orsuspensions, in liquid prior to use can also be prepared. Thepreparation can also be emulsified.

The active ingredient can be mixed with excipients which arepharmaceutically acceptable and compatible with the active ingredientand in amounts suitable for use in the therapeutic methods describedherein. Suitable excipients include, for example, water, saline,dextrose, glycerol, ethanol or the like and combinations thereof. Inaddition, if desired, the composition can contain minor amounts ofauxiliary substances such as wetting or emulsifying agents, pH bufferingagents and the like which enhance the effectiveness of the activeingredient.

Use of timed release or sustained release delivery systems are alsoincluded in the invention. A sustained-release matrix, as used herein,is a matrix made of materials, usually polymers, which are degradable byenzymatic or acid/base hydrolysis or by dissolution. Once inserted intothe body, the matrix is acted upon by enzymes and body fluids. Thesustained-release matrix desirably is chosen from biocompatiblematerials such as liposomes, polylactides (polylactic acid),polyglycolide (polymer of glycolic acid), polylactide co-glycolide(co-polymers of lactic acid and glycolic acid) polyanhydrides,poly(ortho)esters, polyproteins, hyaluronic acid, collagen, chondroitinsulfate, carboxylic acids, fatty acids, phospholipids, polysaccharides,nucleic acids, polyamino acids, amino acids such as phenylalanine,tyrosine, isoleucine, polynucleotides, polyvinyl propylene,polyvinylpyrrolidone and silicone. A preferred biodegradable matrix is amatrix of one of either polylactide, polyglycolide, or polylactideco-glycolide (co-polymers of lactic acid and glycolic acid).

The chimeric molecules and agents described herein can be administeredindividually, in combinations with each other, or in combination withother treatments, as will be apparent to one of skill in the art. Theindividual domains of the chimeric molecules, or individual molecularstructures of the agent described herein, can be administered separatelyor simultaneously to the cell or organism. Formation of the chimericmolecules or agent of the invention, from separate domains or molecularstructures, can occur prior to administering to the cell or organism (exvivo or in vitro assembly), or the separate domains or molecularstructures can be administered to the cell or organism separately andallowed to assemble as chimeric molecules, or as the agent of theinvention, in the cell or organism (in vivo assembly).

Furthermore, one or more chimeric molecules and/or agents of theinvention can be administered to a cell or organism to treat or preventan infection by one or more pathogens. To minimize undesirable effects,one or more pathogen detector or pathogen-induced product detectormolecules can optionally be administered together with one or moreeffector molecules, such that detection of a pathogen orpathogen-induced product by the detector molecule(s) directly orindirectly stimulates, activates, facilitates, or upregulates theeffector molecule(s). For example and without limitation: one or moredetector molecules can be joined to one or more effector molecules suchthat binding to a pathogen or pathogen-induced product activates orfacilitates the function of the effector molecule(s); a detectormolecule can be a genetic promoter which is operatively linked to a genethat encodes an effector molecule; a pathogen or pathogen-inducedproduct can affect a detector molecule, which then stimulates,activates, facilitates, or upregulates the effector molecule(s); apathogen or pathogen-induced product can affect a detector molecule,which then acts via one or more naturally occurring molecules tostimulate, activate, facilitate, or upregulate the effector molecule(s);the detector and effector molecules can be the same molecule, forexample and without limitation, a molecule that binds to one or morepathogens or pathogen components, thereby interfering with the pathogensor pathogen components; the detector and/or effector molecules can bindto or interact with one or more naturally occurring molecules, therebymaking use of the pathogen-detection,pathogen-induced-product-detection, or anti-pathogen properties of saidnaturally occurring molecules.

As will be appreciated by one of skill in the art, the chimericmolecule, agent, domains of the chimeric molecule, or molecularstructures of the agent, can be administered alone or as admixtures withconventional excipients, as described supra, and which do notdeleteriously react with the chimeric molecule or agent. Suchpreparations can be mixed with auxilliary agents such a lubricants,preservatives, stablilizers, wetting agents, emulsifiers, buffers,coloring, and/or aromatic substances and the like, which also do notdeleteriously react with the chimeric molecules or agents of theinvention. Furthermore, the preparations can also be combined with otheractive substances to reduce metabolic degradation, as desired.

The dosage and frequency (single or multiple dosages) administered tothe cell or organism can vary depending on a variety of factors,including the type of pathogen, duration of pathogen infection, extentof disease associated with pathogen infection, weight and health of therecipient and the route of administration of the composition. Thoseskilled in the art will be readily able to determine suitable dosagesand frequencies using standard techniques.

As used herein, the term “therapeutically effective amount” means thetotal amount of each active component of the composition or method thatis sufficient to show a meaningful benefit to the recipient, i.e.,treatment, healing, prevention or amelioration of the relevant diseaseor disorder, or an increase in rate of treatment, healing, prevention oramelioration of such diseases or disorders. When applied to acombination, the term refers to combined amounts of the activeingredients that result in the therapeutic effect, whether administeredin combination, serially or simultaneously.

Other methods of treatment include gene therapy. Gene transfer methodsfor gene therapy fall into three broad categories: physical (e.g.,electroporation, direct gene transfer and particle bombardment),chemical (e.g., lipid-based carriers, or other non-viral vectors) andbiological (e.g., virus-derived vector and receptor uptake). Forexample, non-viral vectors can be used which include liposomes coatedwith DNA. Such liposome/DNA complexes can be directly injectedintravenously into the patient. Additionally, vectors or the “naked” DNAof the gene can be directly injected into the desired organ, tissue ortumor for targeted delivery of the therapeutic DNA.

Gene therapy methodologies can also be described by delivery site.Fundamental ways to deliver genes include ex vivo gene transfer, in vivogene transfer, and in vitro gene transfer. In ex vivo gene transfer,cells are taken from the patient and grown in cell culture. The DNA istransfected into the cells, the transfected cells are expanded in numberand then reimplanted in the patient. In in vitro gene transfer, thetransformed cells are cells growing in culture, such as tissue culturecells, and not particular cells from a particular patient. These“laboratory cells” are transfected, the transfected cells are selectedand expanded for either implantation into a patient or for other uses.

In vivo gene transfer involves introducing the DNA into the cells of thepatient when the cells are within the patient. Methods include usingvirally-mediated gene transfer using a noninfectious virus to deliverthe gene in the patient or injecting naked DNA into a site in thepatient and the DNA is taken up by a percentage of cells in which thegene product protein is expressed. Additionally, other methods such asuse of a “gene gun,” can be used for in vitro insertion of the DNA orregulatory sequences controlling production of the chimeric protein oragent described herein.

Chemical methods of gene therapy can involve a lipid based compound, notnecessarily a liposome, to transfer the DNA across the cell membrane.Lipofectins or cytofectins, lipid-based positive ions that bind tonegatively charged DNA, make a complex that can cross the cell membraneand provide the DNA into the interior of the cell. Another chemicalmethod uses receptor-based endocytosis, which involves binding aspecific ligand to a cell surface receptor and enveloping andtransporting it across the cell membrane. The ligand binds to the DNAand the whole complex is transported into the cell. The ligand genecomplex is injected into the blood stream and then target cells thathave the receptor will specifically bind the ligand and transport theligand-DNA complex into the cell.

Many gene therapy methodologies employ viral vectors to insert genesinto cells. For example, altered retrovirus vectors have been used in exvivo methods to introduce genes into peripheral and tumor-infiltratinglymphocytes, hepatocytes, epidermal cells, myocytes, or other somaticcells. These altered cells are then introduced into the patient toprovide the gene product from the inserted DNA.

Viral vectors have also been used to insert genes into cells using invivo protocols. To direct the tissue-specific expression of foreigngenes, cis-acting regulatory elements or promoters that are known to betissue-specific can be used. Alternatively, this can be achieved usingin situ delivery of DNA or viral vectors to specific anatomical sites invivo. For example, gene transfer to blood vessels in vivo was achievedby implanting in vitro transduced endothelial cells in chosen sites onarterial walls. The virus infected surrounding cells which alsoexpressed the gene product. A viral vector can be delivered directly tothe in vivo site, by a catheter for example, thus allowing only certainareas to be infected by the virus, and providing long-term, sitespecific gene expression.

Viral vectors that have been used for gene therapy protocols include butare not limited to, retroviruses, other RNA viruses such as poliovirusor Sindbis virus, adenovirus, adeno-associated virus, herpes viruses,SV40, vaccinia and other DNA viruses. Replication-defective murineretroviral vectors are the most widely utilized gene transfer vectors.Retroviral vector systems exploit the fact that a minimal vectorcontaining the 5′ and 3′ LTRs and the packaging signal are sufficient toallow vector packaging, infection and integration into target cellsproviding that the viral structural proteins are supplied in trans inthe packaging cell line. Fundamental advantages of retroviral vectorsfor gene transfer include efficient infection and gene expression inmost cell types, precise single copy vector integration into target cellchromosomal DNA, and ease of manipulation of the retroviral genome.

Mechanical methods of DNA delivery include fusogenic lipid vesicles suchas liposomes or other vesicles for membrane fusion, lipid particles ofDNA incorporating cationic lipid such as lipofectin, polylysine-mediatedtransfer of DNA, direct injection of DNA, such as microinjection of DNAinto germ or somatic cells, pneumatically delivered DNA-coatedparticles, such as the gold particles used in a “gene gun,” andinorganic chemical approaches such as calcium phosphate transfection.Particle-mediated gene transfer methods were first used in transformingplant tissue. With a particle bombardment device, or “gene gun,” amotive force is generated to accelerate DNA-coated high densityparticles (such as gold or tungsten) to a high velocity that allowspenetration of the target organs, tissues or cells. Particle bombardmentcan be used in in vitro systems, or with ex vivo or in vivo techniquesto introduce DNA into cells, tissues or organs. Another method,ligand-mediated gene therapy, involves complexing the DNA with specificligands to form ligand-DNA conjugates, to direct the DNA to a specificcell or tissue.

The DNA of the plasmid may or may not integrate into the genome of thecells. Non-integration of the transfected DNA would allow thetransfection and expression of gene product proteins in terminallydifferentiated, non-proliferative tissues for a prolonged period of timewithout fear of mutational insertions, deletions, or alterations in thecellular or mitochondrial genome. Long-term, but not necessarilypermanent, transfer of therapeutic genes into specific cells can providetreatments for genetic diseases or for prophylactic use. The DNA couldbe re-injected periodically to maintain the gene product level withoutmutations occurring in the genomes of the recipient cells.Non-integration of exogenous DNA can allow for the presence of severaldifferent exogenous DNA constructs within one cell with all of theconstructs expressing various gene products.

Electroporation for gene transfer uses an electrical current to makecells or tissues susceptible to electroporation-mediated mediated genetransfer. A brief electric impulse with a given field strength is usedto increase the permeability of a membrane in such a way that DNAmolecules can penetrate into the cells. This technique can be used in invitro systems, or with ex vivo or in vivo techniques to introduce DNAinto cells, tissues or organs.

Carrier mediated gene transfer in vivo can be used to transfect foreignDNA into cells. The carrier-DNA complex can be conveniently introducedinto body fluids or the bloodstream and then site-specifically directedto the target organ or tissue in the body. Both liposomes andpolycations, such as polylysine, lipofectins or cytofectins, can beused. Liposomes can be developed which are cell-specific ororgan-specific and thus the foreign DNA carried by the liposome will betaken up by target cells. Injection of immunoliposomes that are targetedto a specific receptor on certain cells can be used as a convenientmethod of inserting the DNA into the cells bearing the receptor. Anothercarrier system that has been used is the asialoglycoportein/polylysineconjugate system for carrying DNA to hepatocytes for in vivo genetransfer.

The transfected DNA can also be complexed with other kinds of carriersso that the DNA is carried to the recipient cell and then resides in thecytoplasm or in the nucleoplasm. DNA can be coupled to carrier nuclearproteins in specifically engineered vesicle complexes and carrieddirectly into the nucleus.

Chimeric molecules or agents of the invention can optionally be targetedto certain cells within an organism, for example and without restrictionby using a liposome vector, viral vector, or other delivery vector thattargets a ligand specifically expressed on said cells, or by using acell-type-specific promoter operatively linked to a polynucleotidesequence encoding a chimeric molecule or agent of the invention, as willbe readily appreciated by one of skill in the art.

The concentration, dose, and duration of treatment with chimericmolecules or agents of the invention can be controlled to maximize thetherapeutic benefit while minimizing toxicity or undesirableside-effects. Methods of achieving such control will be readilyappreciated by one of skill in the art and include, without restriction,the administered dose of chimeric molecules or agents of the invention,frequency of administration, number of adminstrations, induciblepromoters, molecular structures to control rates of metabolism by theliver and excretion by the kidneys, mRNA stability signals,ubiquitination signals or other protein stability signals, and deliveryvector.

Suitable recipients of the agents described herein include animals,specifically mammals, such as humans, non-human primates, rodents,cattle, and the like. Also included are avian species, fish, plants,insects and prokaryotes, as will be readily appreciated by one of skillin the art.

Furthermore, it is preferred that these chimeric molecules and agentshave minimum toxic side-effects. Even more preferred, the chimericmolecules and agents of the invention have no toxic side-effects.Minimum toxic side-effects can be assessed by those of skill in art.Tolerable toxic side-effects allow the recipient to receive treatmentthat is effective in preventing or treating a pathogen infection, butwhich does not cause irreparable or intolerable injury to the recipient.Preferably, the recipient cell or organism exhibits or suffers nodeleterious toxic side-effects from administration of the treatment,while sufficiently treating or preventing a pathogen infection.

Optionally, chimeric molecules or agents of the invention can beadministered together with stimuli that induce latent viruses toupregulate viral gene expression, thereby enhancing the effect of thechimeric molecules or agents on infected cells, as will be readilyappreciated by one of skill in the art.

It is also considered that some of the chimeric molecules and agentsdescribed herein can treat illnesses other than pathogen infections andthat similar therapeutic agents can be designed that will treatadditional illnesses other than pathogen infections. Illnesses that canbe treated by chimeric molecules or agents described herein, or bysimilar therapeutic agents, include, for example and withoutrestriction, the following: cancer, such as lymphomas, carcinomas andsarcomas; autoimmune diseases, such as rheumatoid arthritis, lupus,transplant rejection, and multiple sclerosis; inflammatory disorderssuch as those associated with hypersensitivity or Crohn's disease (N.Inohara et al. (2003) Journal of Biological Chemistry, PMID: 12514169);primary immunodeficiency diseases; neural disorders such as ischemicneuron injury (W. Paschen and J. Doutheil (1999) J. Cereb. Blood FlowMetab. 19, 1-18), Alzheimer's disease (K. Imaizumi et al. (2001)Biochimica et Biophysica Acta 1536, 85-96; T. Kudo et al. (2002) Ann.N.Y. Acad. Sci. 977, 349-355), Huntington's disease, and Parkinson'sdisease; diabetes (S. Oyadomari et al. (2002) Apoptosis 7, 335-345);cystic fibrosis (M. H. Glickman and A. Ciechanover (2002) Physiol. Rev.82, 373-428; K. M. Sakamoto (2002) Molecular Genetics and Metabolism 77,44-56); atherosclerosis (C. Patterson and D. Cyr (2002) Circulation 106,2741-2746); and the like. For example, detection domains of chimericmolecules or agents can detect apoptosis signals, endoplasmic reticulumstress signals, inflammatory response signals, protein aggregation,cell-cycle-control signals, specific illness-associated molecularepitopes, or other signals associated with illnesses such as thoselisted supra. Effector domains of said chimeric molecules or agents canbe stimulated or induced by said detection domains to affect apoptosispathways, inflammatory-response pathways, unfolded-proteinresponse-pathways, endoplasmic-reticulum-associated-proteindegradation-response pathways, ubiquitin-proteasome pathways,stress-response pathways, or other pathways such that the illness isslowed, alleviated, cured, or prevented.

Chimeric molecules or agents of the invention can be used to detectpathogens, pathogen components, pathogen products, or other molecules.For example and without restriction, chimeric molecules having a caspaseeffector domain and a detector domain that recognizes a polyvalentpathogen, pathogen component, pathogen product, cancer antigen, otherantigen, or other molecule can be used to detect said pathogen, pathogencomponent, pathogen product, cancer antigen, other antigen, or moleculein a sample. Colorimetric, fluorometric, and other assays for caspaseactivity (for example, those from R&D Systems) are well known to thoseof skill in the art. An increase in caspase activity of the chimericmolecules or agents indicates that said pathogen, pathogen component,pathogen product, cancer antigen, other antigen, or molecule is presentin a sample and can optionally be used to determine the concentration ofsaid pathogen, pathogen component, pathogen product, cancer antigen,other antigen, or molecule in said sample, as will be readilyappreciated by one of skill in the art. Optionally, another effectordomain such as a kinase that activates upon crosslinking can be usedwith a suitable assay, as will be readily appreciated by one of skill inthe art.

The present invention is further illustrated by the following examples,which more specifically illustrate the invention.

EXEMPLIFICATION Example 1

Materials: dsRNA-Activated Caspases

Plasmids encoding human procaspase 3 (NCBI Accession #U26943) and aminoacids 1-125 of human FADD (#U24231) were provided by D. M. Spencer,Baylor College of Medicine. A plasmid encoding human protein kinase R(#U50648) was provided by E. F. Meurs, Institut Pasteur. The mammalianexpression vector pTRE2hyg, HeLa Tet-On™ human cell line, doxycycline,and tetracycline-free fetal bovine serum were obtained from Clontech.The pCR®2.1-TOPO vector was supplied by Invitrogen. PCR primers,LIPOFECTIN® reagent, and PLUS reagent were obtained from Gibco BRL/LifeTechnologies/Invitrogen. Polyclonal goat IgG antibodies specific forhuman caspase 3 were from R&D Systems, and HRP-conjugated rabbitantibodies specific for goat IgG (H+L) were from Zymed. Polyclonalrabbit IgG antibodies specific for human FADD were from UpstateBiotechnology, and HRP-conjugated goat antibodies specific for rabbitIgG were from Santa Cruz Biotechnology. CellTiter 96® AQueous OneSolution was obtained from Promega. Poly(I)•poly(C) double-stranded RNAwas from Amersham Pharmacia. Synthesis of dsRNA-Activated Caspases: PCRproduct 7 FIG. 7 illustrates the strategy for the synthesis of PCRproduct 7, which encodes a novel dsRNA-activated caspase. ThedsRNA-binding domain from PKR (amino acids 1-174) was fused in framewith a short flexible polypeptide linker (S-G-G-G-S-G (SEQ ID NO: 1))and full-length caspase-3. A Kozak sequence and stop codon were includedas shown. BamH I and Mlu I restriction sites were included at the endsfor ease of insertion into the pTRE2hyg vector. PCR 1 used the indicated5′ and 3′ PCR primers to PCR amplify the region encoding amino acids1-174 of PKR from the provided plasmid. PCR 2 used the indicated 5′ and3′ PCR primers to PCR amplify the coding sequence of caspase-3 from theprovided plasmid. PCR 7 used gel-purified products of PCR 1 and 2, 5′primer from PCR 1, and 3′ primer from PCR 2, to create the desiredproduct by splicing by overlap extension (C. W. Dieffenbach and G. S.Dveksler (eds.), PCR Primer: A Laboratory Manual (1995, Cold SpringHarbor Laboratory Press, Plainview, N.Y.).).

Synthesis of dsRNA-Activated Caspases: PCR Product 8

FIG. 8 illustrates the strategy for the synthesis of PCR product 8,which encodes a novel dsRNA-activated caspase. The dsRNA-binding domainfrom PKR (amino acids 1-174) and part of the natural linker region fromPKR (amino acids 175-181) were fused in frame with full-lengthcaspase-3. A Kozak sequence and stop codon were included as shown. BamHI and Mlu I restriction sites were included at the ends for ease ofinsertion into the pTRE2hyg vector. PCR 3 used the indicated 5′ and 3′PCR primers to PCR amplify the region encoding amino acids 1-181 of PKRfrom the provided plasmid. PCR 6 used the indicated 5′ and 3′ PCRprimers to copy the coding sequence of caspase-3 from the providedplasmid. PCR 8 used gel-purified products of PCR 3 and 6, 5′ primer fromPCR 3, and 3′ primer from PCR 6, to create the desired product bysplicing by overlap extension.

Synthesis of dsRNA-Activated Caspase Activators: PCR Product 9

FIG. 9 illustrates the strategy for the synthesis of PCR product 9,which encodes a novel dsRNA-activated caspase activator. ThedsRNA-binding domain from PKR (amino acids 1-174) and part of thenatural linker region from PKR (amino acids 175-181) were fused in framewith amino acids 1-125 of FADD, which includes the death effector domain(DED) that binds to procaspase-8. When two or more copies of the proteinencoded by PCR 9 are cross-linked by dsRNA, they will cross-link andactivate endogenous (pro)caspase-8. A Kozak sequence and stop codon wereincluded as shown. BamH I and Mlu I restriction sites were included atthe ends for ease of insertion into the pTRE2hyg vector. PCR 3 used theindicated 5′ and 3′ PCR primers to copy the region encoding amino acids1-181 of PKR from the provided plasmid. PCR 4 used the indicated 5′ and3′ PCR primers to PCR amplify the region encoding amino acids 1-125 ofFADD from the provided plasmid. PCR 9 used gel-purified products of PCR3 and 4, 5′ primer from PCR 3, and 3′ primer from PCR 4 to create thedesired product by splicing by overlap extension.

Synthesis of dsRNA-Activated Caspase Activators: PCR Product 10

FIG. 10 illustrates the strategy for the synthesis of PCR product 10,which encodes a novel dsRNA-activated caspase activator. ThedsRNA-binding domain from PKR (amino acids 1-174) was fused in framewith a short flexible polypeptide linker (S-G-G-G-S-G (SEQ ID NO: 1))and amino acids 1-125 of FADD, which includes the death effector domain(DED) that binds to procaspase-8. When two or more copies of the proteinencoded by PCR 10 are cross-linked by dsRNA, they will cross-link andactivate endogenous (pro)caspase-8. A Kozak sequence and stop codon wereincluded as shown. BamH I and Mlu I restriction sites were included atthe ends for ease of insertion into the pTRE2hyg vector. PCR 1 used theindicated 5′ and 3′ PCR primers to PCR amplify the region encoding aminoacids 1-174 of PKR from the provided plasmid. PCR 5 used the indicated5′ and 3′ PCR primers to PCR amplify the region encoding amino acids1-125 of FADD from the provided plasmid. PCR 10 used the gel-purifiedproducts of PCR 1 and 5, 5′ primer from PCR 1, and 3′ primer from PCR 5to create the desired product by splicing by overlap extension.

Cloning of PCR Products 7 through 10

PCR products 7, 8, 9, and 10 were gel purified and inserted into theInvitrogen pCR®2.1-TOPO vector following the manufacturer's protocol.The inserts are sequenced on both strands by the Nucleic Acid/ProteinResearch Core Facility at the Children's Hospital of Philadelphia. ThepCR®2.1-TOPO vectors containing PCR products 7 through 10 were digestedby BamH I and Mlu I restriction enzymes, and the fragments correspondingto PCR products 7 through 10 were gel purified. The pTRE2hyg vector,shown schematically in FIG. 11, was also digested by BamH I and Mlu I,and the larger resulting fragment gel purified. Then the digested PCRproducts 7 through 10 were ligated into the digested vector to createexpression vectors for PCR 7, 8, 9, and 10. The vectors include adoxycycline or tetracycline-inducible promoter for the inserted gene, aswell as a hygromycin resistance gene for selection of transfected cells.A Clontech-supplied control vector has a luciferase gene inserted afterthe inducible promoter. The inserted region of the new vectors wassequenced on both strands by the Nucleic Acid/Protein Research CoreFacility at the Children's Hospital of Philadelphia. All of the vectorswith the inserted genes were linearized for transfection using the Fsp Irestriction enzyme and are shown in the DNA gel electrophoresis photo inFIG. 11.

Cell Transfections with dsRNA-Activated Caspases and dsRNA-ActivatedCaspases Acitvators

The Clontech Tet-On HeLa human cell line contains the rtTA regulatoryprotein necessary for the proper functioning of the tetracycline ordoxycycline-inducible promoters. Cells were maintained using standardtissue culture practices, humidified incubators at 37° C. and 5% CO₂,and DMEM culture medium containing 10% tetracycline-free fetal bovineserum, 100 μM nonessential amino acids, 1 mM sodium pyruvate, 4 mML-glutamine, 100 units/ml penicillin G, 100 μg/ml streptomycin, 250ng/ml amphotericin B, and 100 μg/ml G418.

As shown in FIG. 12, the linearized pTRE2hyg-derived vectors withinserted PCR 7, 8, 9, 10, or luciferase are transfected into the HeLaTet-On™ cells. The transfections use LIPOFECTIN® and PLUS reagents fromInvitrogen and follow Invitrogen's recommended protocol for HeLa cells.One day after transfection, 250 μg/ml hygromycin was added to the cellculture medium to kill any cells that had not been stably transfectedwith the vectors, and the cells were permanently kept in thisconcentration of hygromycin as a precaution against the possibility thatthe cells might lose the transfected genes.

The pools of hygromycin-resistant cells that resulted from eachtransfection are presumably genetically heterogeneous, with differentcells having different copy numbers of the inserted vector or having thevector inserted into different regions of the cellular genome.Therefore, genetically homogeneous clonal cell populations wereisolated. Limiting dilutions of the pools of transfected cells are usedto deposit approximately 1 cell per well into 96-well plates, and thecells are allowed to multiply. Wells that appear to have received morethan one initial cell were disregarded. The resulting clonal cellpopulations were designated HeLa 7-x, 8-x, 9Ax, or 10-x; the firstnumber indicates which PCR product from FIGS. 7-10 was transfected intothe cells, and the x is replaced with the cell clone number. Forexample, cell line HeLa 7-3 indicates PCR product 7, cell clone 3.

Protein Expression in Transfected Cells

Western blots were used to analyze the cell clones. PKR-Caspase-3 fusionproteins (deriving from PCR 7 and 8) were detected usingcaspase-3-specific polyclonal goat IgG antibodies from R&D Systems, andPKR-FADD fusion proteins (deriving from PCR 9 and 10) were detectedusing FADD-specific polyclonal rabbit IgG antibodies from UpstateBiotechnology. Cells were cultured for two days either with or withoutdoxycyline, and the proteins extracted from the cells and analyzed byWestern blot following the manufacturers' protocol.

The Western blot in FIG. 13 illustrates that doxycycline induced cellstransfected with the PCR-7-containing vector to express thecorresponding dsRNA-activated caspase. Cells were cultured with either10 μg/ml doxycycline or no doxycycline for two days, and the Westernblots were used to probe the cell extracts with anti-caspase-3antibodies. The 32-kDa natural (pro)caspase 3 was visible in all thecells, either with or without doxycycline. For each cell clone shown,doxycycline up-regulates expression of the dsRNA-activated caspase,which has approximately the predicted size and contains caspase-3epitopes recognized by the antibodies.

The Western blot in FIG. 14 illustrates that doxycycline induces cellstransfected with the PCR-8-containing vector to express thecorresponding dsRNA-activated caspase. Cells were cultured with either10 μg/ml doxycycline or no doxycycline for two days, and then Westernblots were used to probe the cell extracts with anti-caspase-3antibodies. The 32-kDa natural (pro)caspase 3 is visible in all thecells, either with or without doxycycline. For cell clones 8-9, 8-13,and 8-17, doxycycline up-regulates expression of the dsRNA-activatedcaspase, which has approximately the predicted size and containscaspase-3 epitopes recognized by the antibodies.

The Western blot in FIG. 15 illustrates that doxycycline induces cellstransfected with the PCR-9-containing vector to express thecorresponding dsRNA-activated caspase activator. Cells were culturedwith either 1 μg/ml doxycycline or no doxycycline for two days, and thenWestern blots were used to probe the cell extracts with anti-FADDantibodies. The 28-kDa natural FADD is visible in all the cells, eitherwith or without doxycycline. For each cell clone shown, doxycyclineup-regulates expression of the dsRNA-activated caspase activator, whichhas approximately the predicted size and contains FADD epitopesrecognized by the antibodies.

The Western blot in FIG. 16 illustrates that doxycycline induces cellstransfected with the PCR-10-containing vector to express thecorresponding dsRNA-activated caspase activator. Cells are cultured witheither 10 μg/ml doxycycline or no doxycycline for two days, and thenWestern blots are used to probe the cell extracts with anti-FADDantibodies. The 28-kDa natural FADD is visible in all the cells, eitherwith or without doxycycline. For each cell clone shown, doxycyclineupregulates expression of the dsRNA-activated caspase activator, whichhas approximately the predicted size and contains FADD epitopesrecognized by the antibodies.

Doxycycline Concentration Dependent Expression in Transfected Cells

The Western blot in FIG. 17 demonstrates that the doxycyclineconcentration controls the level of dsRNA-activated caspase (or caspaseactivator) expression in transfected cells. Cell clone 7-6 contains PCR7, clone 8-13 contains PCR 8, clone 10-6 contains PCR 10, and 9A is apool of clones that contain PCR 9 but have not been separated intoindividual clonal populations by limiting dilution. Untransfected HeLacells were used as a control. Cells were cultured with 0, 0.01, 0.1, 1,or 10 μg/ml doxycycline for two days, and then Western blots were usedto probe the cell extracts with anti-caspase-3 or anti-FADD antibodies.Increasing the doxycycline concentration generally increases theexpression level of the dsRNA-activated caspase (or caspase activator)relative to natural caspase 3 or FADD.

Toxicity Assays

The toxicity of the transfected genes was assayed as follows. Cells wereadded to 96-well plates at an initial density of 5×10⁴ cells/ml and with100 μl of medium per well. Different expression levels of thetransfected genes were induced by adding 0, 0.01, 0.1, 1, or 10 μg/mldoxycycline. The cell numbers were estimated after three days usingPromega CellTiter 96® AQueous One Solution, which is bioreduced by livecells into a colored formazan product. The manufacturer's recommendedprotocol was followed. After subtracting the background absorbance foundin wells with medium but no cells, the absorbance at 492 nm isapproximately linear with the number of live cells. All assays wereperformed in quadruplicate to reduce statistical variations.

FIG. 18 illustrates the toxicity of dsRNA-activated caspase (PCR 7)levels induced by different concentrations of doxycycline. At alldoxycycline concentrations, the metabolism of cell clones 7-1, 7-4, and7-6 was approximately the same as that of untransfected HeLa cells,indicating little or no toxicity.

FIG. 19 illustrates the toxicity of dsRNA-activated caspase (PCR 8)levels induced by different concentrations of doxycycline. At alldoxycycline concentrations, the metabolism of cell clones 8-9, 8-13, and8-17 was approximately the same as that of untransfected HeLa cells,indicating little or no toxicity.

FIG. 20 illustrates the toxicity of dsRNA-activated caspase activator(PCR 9) levels induced by different concentrations of doxycycline. Thereappears to be some toxicity at high expression levels, thus thisdsRNA-activated caspase activator could be used against pathogens atlower levels.

FIG. 21 illustrates the toxicity of dsRNA-activated caspase activator(PCR 10) levels induced by different concentrations of doxycycline.There appears to be some toxicity at high expression levels, thus thisdsRNA-activated caspase activator could be used against pathogens atlower levels.

dsRNA-Dependent Apoptosis

Cells were tested with poly(I)•poly(C) dsRNA to determine if apoptosiswas induced as expected. Cells were cultured either with or without 10μg/ml doxycycline for two days. Then the dsRNA was transfected into thecells at a concentration of approximately 7.5 μg/ml using theLIPOFECTIN® and PLUS reagents from Invitrogen and following Invitrogen'srecommended protocol for transfecting HeLa cells. Control cells weretransfected using the same protocol but without any dsRNA. Cells thathad previously been cultured with doxycycline remained in doxycycline,and cells that had not previously been cultured in doxycycline were nottreated with doxycycline. Approximately 20 hours after the dsRNAtransfections, the cells were photographed using a CCD camera attachedto a 400× inverted phase-contrast microscope. Healthy cells tend tospread out, whereas apoptotic cells round up and appear to have brightgranulated interiors.

The photographs in FIG. 22 demonstrate the dsRNA-activated caspase incell clone 8-13. Cells without dsRNA appear healthy, regardless ofdoxycycline treatment. Cells without doxycyline but with dsRNA appeargenerally healthy but include some apoptotic cells, possibly due to thelow-level expression of the dsRNA-activated caspase even in the absenceof doxycycline. Cells with both doxycycline and dsRNA exhibit widespreadapoptosis as expected.

The photographs in FIG. 23 demonstrate the dsRNA-activated caspase incell clone 8-9. Cells without dsRNA appear healthy, regardless ofdoxycycline treatment. Cells without doxycyline but with dsRNA appeargenerally healthy but include some apoptotic cells, possibly due to thelow-level expression of the dsRNA-activated caspase even in the absenceof doxycycline. Cells with both doxycycline and dsRNA exhibit widespreadapoptosis as expected; the apparently healthy cells that remain may nothave received any of the dsRNA.

The photographs in FIG. 24 illustrate untransfected HeLa cells used as acontrol for the dsRNA-activated caspase transfection experimentsdescribed supra. Cells either with or without doxycycline and eitherwith or without dsRNA appeared generally healthy, with a limited numberof round or apoptotic cells visible in each of the four cases. Whilethere were some variations among the four populations of cells that mayor may not be statistically significant, the widespread apoptosis thatwas visible in clones 8-9 and 8-13 treated with both doxycycline anddsRNA does not occur with the untransfected HeLa cells.

Example 2

Materials: Interferon-Inducible Defense Genes

Plasmids encoding human Hdj-1 (NCBI Accession #X62421) and human Hsp70(#M11717 M15432) were provided by R. I. Morimoto, NorthwesternUniversity. A plasmid encoding human Hsp90 (#M16660) was provided by R.D. Mosser, Biotechnology Research Institute, National Research Councilof Canada. The vector pISRE-Luc was obtained from Stratagene. Themammalian expression vector pCMV/Bsd and cloning vector pCR®2.1-TOPOwere obtained from Invitrogen. PCR primers, LIPOFECTIN® reagent, andPLUS reagent were obtained from Gibco BRL/Life Technologies/Invitrogen.The H1-HeLa human cell line (CRL-1958) was obtained from ATCC. Humaninterferon-alpha is from Sigma.

Synthesis of Interferon-Inducible Defense Genes

FIG. 26 illustrates how an interferon-inducible vector was created byadding an interferon-inducible promoter and poly-A sequence to theInvitrogen pCMV/Bsd blasticidin-resistance vector. A multiple cloningsequence between the new interferon-inducible promoter and poly-Asequence permits one to add any gene, such as genes for heat shockproteins Hdj-1, Hsp70, Hsp90, luciferase (as a control), or other geneswith anti-pathogen effects.

Using the strategy shown in FIG. 27, the SV40 poly-A sequence was copiedfrom pCMV/Bsd via PCR 11 with the illustrated primers. The product ofPCR 11 was gel purified and inserted into the Invitrogen pCR®2.1-TOPOvector following the manufacturer's protocol. The inserts were sequencedon both strands by the Nucleic Acid/Protein Research Core Facility atthe Children's Hospital of Philadelphia. The pCR®2.1-TOPO vectorcontaining PCR product 11 was digested by Hind III and Kas I restrictionenzymes, and the fragment corresponding to PCR product 11 was gelpurified. The pCMV/Bsd vector, shown schematically in FIG. 27, was alsodigested by Hind III and Kas I, and the larger resulting fragment wasgel purified. The digested PCR product 11 was ligated into the digestedvector to create modified pCMV/Bsd. The inserted region of the newvector was sequenced on both strands by the Nucleic Acid/ProteinResearch Core Facility at the Children's Hospital of Philadelphia.

Using the strategy shown in FIG. 28, an interferon-inducible promotercontaining multiple interferon-stimulated response elements (ISREs) wascloned from the Stratagene vector pISRE-Luc via PCR 12 with theillustrated primers. The product of PCR 12 was gel purified and insertedinto the Invitrogen pCR®2.1-TOPO vector following the manufacturer'sprotocol. The inserts were sequenced on both strands by the NucleicAcid/Protein Research Core Facility at the Children's Hospital ofPhiladelphia. The pCR®2.1-TOPO vector containing PCR product 12 wasdigested by BamH I and Sal I restriction enzymes, and the fragmentcorresponding to PCR product 12 was gel purified. The modified pCMV/Bsdvector, shown schematically in FIG. 28, was also digested by BamH I andSal I, and the larger resulting fragment was gel purified. Then thedigested PCR product 12 was ligated into the digested vector to createpCMV/Bsd/ISRE, a general-purpose interferon-inducible mammalianexpression vector. The inserted region of the new vector was sequencedon both strands by the Nucleic Acid/Protein Research Core Facility atthe Children's Hospital of Philadelphia. Any desired gene can beinserted into this new interferon-inducible vector, transfected intomammalian cells, and induced by interferon.

Synthesis of Interferon-Inducible Defense Genes: Hdj-1

Using the strategy shown in FIG. 29, the gene for heat shock proteinHdj-1 is cloned from the provided plasmid in PCR 13 with the illustratedprimers. The PCR primers are used to add a Kozak sequence as well asBssH II and Mlu I restriction enzyme sites. The product of PCR 13 is gelpurified and inserted into the Invitrogen pCR®2.1-TOPO vector followingthe manufacturer's protocol. The inserts are sequenced on both strandsby the Nucleic Acid/Protein Research Core Facility at the Children'sHospital of Philadelphia. Site-directed mutagenesis is used to correctthe encoded amino acids to the published sequence. The pCR®2.1-TOPOvector containing the corrected PCR product 13 is digested by BssH IIand Mlu I restriction enzymes, and the fragment corresponding to PCRproduct 13 is gel purified. The pCMV/Bsd/ISRE vector, shownschematically in FIG. 29, is also digested by BssH II and Mlu I, and thelarger resulting fragment is gel purified. Then the digested PCR product13 is ligated into the digested vector to create an interferon-inducibleHdj-1 expression vector. The inserted region of the new vector issequenced on both strands by the Nucleic Acid/Protein Research CoreFacility at the Children's Hospital of Philadelphia.

Synthesis of Interferon-Inducible Defense Gene: Hsp70

Using the strategy shown in FIG. 30, the gene for heat shock proteinHsp70 is cloned from the provided plasmid in PCR 14 with the illustratedprimers. The PCR primers are used to add a Kozak sequence as well asBssH II and Mlu I restriction enzyme sites. The product of PCR 14 is gelpurified and inserted into the Invitrogen pCR®2.1-TOPO vector followingthe manufacturer's protocol. The inserts are sequenced on both strandsby the Nucleic Acid/Protein Research Core Facility at the Children'sHospital of Philadelphia. Site-directed mutagenesis is used to correctthe encoded amino acids to the published sequence. The pCR®2.1-TOPOvector containing the corrected PCR product 14 is digested by BssH IIand Mlu I restriction enzymes, and the fragment corresponding to PCRproduct 14 is gel purified. The pCMV/Bsd/ISRE vector, shownschematically in FIG. 30, is also digested by BssH II and Mlu I, and thelarger resulting fragment is gel purified. Then the digested PCR product14 is ligated into the digested vector to create an interferon-inducibleHsp70 expression vector. The inserted region of the new vector issequenced on both strands by the Nucleic Acid/Protein Research CoreFacility at the Children's Hospital of Philadelphia.

Synthesis of Interferon-Inducible Defense Gene: Hsp90

Using the strategy shown in FIG. 31, the gene for heat shock proteinHsp90 is cloned from the provided plasmid in PCR 15 with the illustratedprimers. The PCR primers are used to add a Kozak sequence as well asBssH II and Mlu I restriction enzyme sites. The product of PCR 15 is gelpurified and inserted into the Invitrogen pCR®2.1-TOPO vector followingthe manufacturer's protocol. The inserts are sequenced on both strandsby the Nucleic Acid/Protein Research Core Facility at the Children'sHospital of Philadelphia. Site-directed mutagenesis is used to correctthe encoded amino acids to the published sequence. The pCR®2.1-TOPOvector containing the corrected PCR product 15 is digested by BssH IIand Mlu I restriction enzymes, and the fragment corresponding to PCRproduct 15 is gel purified. The pCMV/Bsd/ISRE vector, shownschematically in FIG. 31, is also digested by BssH II and Mlu I, and thelarger resulting fragment is gel purified. Then the digested PCR product15 is ligated into the digested vector to create an interferon-inducibleHsp90 expression vector. The inserted region of the new vector issequenced on both strands by the Nucleic Acid/Protein Research CoreFacility at the Children's Hospital of Philadelphia.

Synthesis of Interferon-Inducible Defense Gene: Control Gene

Using the strategy shown in FIG. 32, the gene for luciferase was clonedfrom pISRE-Luc in PCR 16 with the illustrated primers. The PCR primerswere used to add a Kozak sequence as well as BssH II and Mlu Irestriction enzyme sites. The product of PCR 16 was gel purified andinserted into the Invitrogen pCR®2.1-TOPO vector following themanufacturer's protocol. The inserts were sequenced on both strands bythe Nucleic Acid/Protein Research Core Facility at the Children'sHospital of Philadelphia. The pCR®2.1-TOPO vector containing PCR product16 was digested by BssH II and Mlu I restriction enzymes, and thefragment corresponding to PCR product 16 was gel purified. ThepCMV/Bsd/ISRE vector, shown schematically in FIG. 32, was also digestedby BssH II and Mlu I, and the larger resulting fragment is gel purified.Then the digested PCR product 16 was ligated into the digested vector tocreate an interferon-inducible luciferase expression vector. Theinserted region of the new vector was sequenced on both strands by theNucleic Acid/Protein Research Core Facility at the Children's Hospitalof Philadelphia.

DNA Gel Electrophoresis Analyses of Interferon-Inducible Defense Genes

The DNA electrophoresis gel photographs in FIG. 33 show the products ofPCR 11 through PCR 16. PCR 11 is the poly-A sequence, PCR 12 is theISRE-containing interferon-inducible promoter, PCR 13 is Hdj-1, PCR 14is Hsp70, PCR 15 is Hsp90, and PCR16 is luciferase.

The DNA electrophoresis gel photograph in FIG. 34 illustrates theinteferon-inducible vectors and genes. The second lane of the gel is thecompleted interferon-inducible vector pCMV/Bsd/ISRE without an insertedgene. Lane 3 is the same vector with Hsp90 inserted, and Lane 4 is thevector with luciferase inserted. The vector in these lanes has beendigested with the restriction enzymes BssH II and Mlu I for ease ofanalysis. The rightmost two lanes are the Hdj-1 and Hsp70 genes insertedinto the Invitrogen pCR®2.1-TOPO vector, digested with EcoR I for easeof analysis. Using the methods described in FIGS. 29 and 30, the Hdj-1and Hsp70 genes are inserted into pCMV/Bsd/ISRE.

Cell Transfections with Interferon-Inducible Defense Genes

H1-HeLa cells are maintained using standard tissue culture practices,humidified incubators at 37° C. and 5% CO₂, and DMEM culture mediumcontaining 10% fetal bovine serum, 100 μM nonessential amino acids, 1 mMsodium pyruvate, 4 mM L-glutamine, 100 units/ml penicillin G, 100 μg/mlstreptomycin, and 250 ng/ml amphotericin B.

The interferon-inducible expression vectors for Hdj-1, Hsp70, Hsp90, andluciferase are linearized and transfected into the H1-HeLa cells. Thetransfections use LIPOFECTIN® and PLUS reagents from Invitrogen andfollow Invitrogen's recommended protocol for HeLa cells. One day afterthe transfection, blasticidin is added to the cell culture medium tokill any cells that have not been stably transfected with the vectors,and the cells are permanently kept in blasticidin as a precautionagainst the possibility that the cells might lose the transfected genes.

The pools of blasticidin-resistant cells that result from eachtransfection are presumably genetically heterogeneous, with differentcells having different copy numbers of the inserted vector or having thevector inserted into different regions of the cellular genome.Therefore, genetically homogeneous clonal cell populations are isolated.Limiting dilutions of the pools of transfected cells are used to depositapproximately 1 cell per well into 96-well plates, and the cells areallowed to multiply. Wells that appear to have received more than oneinitial cell are disregarded.

Protein Expression of Interferon-Inducible Defense Genes in TransfectedCells

Western blots are used to analyze the cell clones. Cells are culturedfor one day either with or without human interferon-alpha, and thenproteins are extracted from the cells and analyzed by Western blot withantibodies specific for human Hdj-1, Hsp70, or Hsp90. Cells induced withinterferon express more of the heat shock protein with which they weretransfected than cells that have not been induced or controluntransfected H1-HeLa cells.

EXAMPLE 3

dsRNA-Activated Caspase Protects H1-HeLa Cells from Rhinovirus

Materials and Methods

H1-HeLa cells (ATCC CRL-1958) were chosen because of their particularsusceptibility to rhinovirus. Cells were maintained using standardtissue culture practices, humidified incubators at 37° C. and 5% CO₂,and DMEM culture medium containing 10% tetracycline-free fetal bovineserum, 100 μM nonessential amino acids, 1 mM sodium pyruvate, 4 mML-glutamine, 100 units/ml penicillin G, 100 μg/ml streptomycin, and 250ng/ml amphotericin B. The vector pTetOn encodes the rtTA regulatoryprotein necessary for the proper functioning of tetracycline ordoxycycline-inducible promoters; it was obtained from BD BioscencesClontech and prepared and linearized following the manufacturer'sdirections.

H1-HeLa cells were co-transfected with 5 μg each of linearized pTetOnand the linearized pTRE2hyg-derived vector that contained PCR 8. Thetransfections used LIPOFECTIN® and PLUS reagents from Invitrogen andfollow Invitrogen's recommended protocol for HeLa cells. One day afterthe transfection, 600 μg/ml G418 and 400 μg/ml hygromycin were added tothe cell culture medium to kill any cells that had not been stablytransfected with the vectors, and the cells were subsequently kept in800 μg/ml G418 and 400 μg/ml hygromycin as a precaution against thepossibility that the cells might lose the transfected genes. Theresulting transfected cells were designated 8S or 8 simultaneous.

Results and Discussion

The Western blot in FIG. 37 demonstrates that doxycycline induced 8Scells to express the dsRNA-activated caspase. Untransfected H1-HeLacells were cultured without doxycycline for two days, and 8S cells werecultured with 0, 1, or 10 μg/ml doxycycline for two days. Western blotswere then used to probe the cell extracts with anti-caspase-3antibodies. The 32-kDa natural (pro)caspase 3 was visible in all thecells, regardless of transfection or doxycycline. For 8S cells, 1 or 10μg/ml doxycycline upregulated expression of the dsRNA-activated caspase,which has approximately the predicted size (FIG. 37, labeled as 53 kDanew protein) and contains caspase-3 epitopes recognized by theantibodies.

To demonstrate the effectiveness of the dsRNA-activated caspase againstvirus, cells were infected with human rhinovirus 14 (ATCC VR-284), asshown in FIG. 38. The stock rhinovirus concentration was determined vialimiting dilutions and plaque assays on untransfected H1-HeLa cells.Control untransfected H1-HeLa cells without doxycycline and 8S H1-HeLacells induced with 10 μg/ml doxycycline were grown in 25-cm² tissueculture flasks. Approximately 300 plaque-forming units (pfu) of viruswere added to flasks of untransfected and transfected cells, while otherflasks were left uninfected as controls. After 7 days of incubation at33° C., all untransfected cell populations exposed to rhinovirus werecompletely dead and detached from their flasks' surfaces (FIG. 38, lowerleft panel). In contrast, transfected 8S H1-HeLa cells that have beenexposed to rhinovirus were alive, attached, and confluent, and they showno signs of infection (FIG. 38, lower right panel). Both untransfectedand transfected cells not exposed to rhinovirus were also confluent andhealthy (FIG. 38, upper left and right panels, respectively). Thus thedsRNA-activated caspase successfully protects HeLa cells against viralinfection and has little or no toxicity. Differences in cell densityamong the various flasks were due to differences in the initial cellseeding densities and therefore are not related to the dsRNA-activatedcaspase.

Example 4

dsRNA-Activated Caspases in Human Embyonic Kidney 293 Cells

Materials and Methods

The 293 TetOn™ cell line (BD Biosciences Clontech) contained the rtTAregulatory protein necessary for the proper functioning of thetetracycline or doxycycline-inducible promoters. Cells were maintainedusing standard tissue culture practices, humidified incubators at 37° C.and 5% CO₂, and DMEM culture medium containing 10% tetracycline-freefetal bovine serum, 100 μM nonessential amino acids, 1 mM sodiumpyruvate, 4 mM L-glutamine, 100 units/ml penicillin G, 100 μg/mlstreptomycin, 250 ng/ml amphotericin B, and 100 μg/ml G418.

The linearized pTRE2hyg-derived vectors with inserted PCR 7, 8, 9, or 10were transfected into the 293 Tet-On™ cells. The transfections usedLIPOFECTIN® and PLUS reagents from Invitrogen and followed Invitrogen'srecommended protocol for HeLa cells. One day after the transfection, 100μg/ml hygromycin was added to the cell culture medium to kill any cellsthat had not been stably transfected with the vectors, and the cellswere subsequently kept in 100 μg/ml G418 and 200 μg/ml hygromycin as aprecaution against the possibility that the cells might lose thetransfected genes.

The pools of hygromycin-resistant cells that result from eachtransfection were presumably genetically heterogeneous, with differentcells having different copy numbers of the inserted vector or having thevector inserted into different regions of the cellular genome.Therefore, genetically homogeneous clonal cell populations wereisolated. Limiting dilutions of the pools of transfected cells were usedto deposit approximately 1 cell per well into 96-well plates, and thecells were allowed to multiply. Wells that appeared to have receivedmore than one initial cell were disregarded. The resulting clonal cellpopulations were designated 293 7-x, 8-x, 9-x, or 10-x; the first numberafter the cell line name indicates which PCR product was transfectedinto the cells, and the x is replaced with the cell clone number. Forexample, cell line 293 7-3 indicates PCR product 7, cell clone 3.

Western blots were used to analyze the cell clones. PKR-caspase 3 fusionproteins (deriving from PCR 7 and 8) were detected usingcaspase-3-specific polyclonal goat IgG antibodies from R&D Systems, andPKR-FADD fusion proteins (deriving from PCR 9 and 10) were detectedusing FADD-specific polyclonal rabbit IgG antibodies from UpstateBiotechnology. Cells were cultured for two days either with or withoutdoxycycline, and then proteins were extracted from the cells andanalyzed by Western blot following the manufacturers' protocols.

Results and Discussion

The Western blot in FIG. 39 demonstrates that doxycycline induces 293cells transfected with the PCR-7- or PCR-8-containing vectors to expressthe corresponding dsRNA-activated caspase. Cells were cultured witheither 10 μg/ml doxycycline or no doxycycline for two days, and thenWestern blots were used to probe the cell extracts with anti-caspase-3antibodies. The 32-kDa natural (pro)caspase 3 was visible in all thecells, either with or without doxycycline. For each cell clone shown,doxycycline upregulated expression of the dsRNA-activated caspase, whichhas approximately the predicted size (FIG. 39, labeled as 53 kDa newprotein) and contains caspase-3 epitopes recognized by the antibodies.

The Western blot in FIG. 40 demonstrates that doxycycline induced 293cells transfected with the PCR-9-containing vector to express thecorresponding dsRNA-activated caspase activator. Cells were culturedwith either 10 μg/ml doxycycline or no doxycycline for two days, andthen Western blots were used to probe the cell extracts with anti-FADDantibodies. The 28-kDa natural FADD was visible in all the cells, eitherwith or without doxycycline. For each cell clone shown, doxycyclineupregulated expression of the dsRNA-activated caspase activator, whichhas approximately the predicted size (FIG. 40, labeled as 41 kDa newprotein) and contains FADD epitopes recognized by the antibodies.

The Western blot in FIG. 41 demonstrates that doxycycline induced 293cells transfected with the PCR-10-containing vector to express thecorresponding dsRNA-activated caspase activator. Cells were culturedwith either 10 μg/ml doxycycline or no doxycycline for two days, andthen Western blots were used to probe the cell extracts with anti-FADDantibodies. The 28-kDa natural FADD was visible in all the cells, eitherwith or without doxycycline. For each cell clone shown, doxycyclineupregulated expression of the dsRNA-activated caspase activator, whichhas approximately the predicted size (FIG. 41, labeled as 41 kDa newprotein) and contains FADD epitopes recognized by the antibodies.

This demonstrates that 293 cells can be induced to express PCR 7, 8, 9,or 10 for two days and illustrates that the corresponding proteins havelimited or no toxicity to uninfected cells.

Example 5

Other Pathogen-Activated Apoptosis Treatments

Materials and Methods

A plasmid encoding human procaspase 3 (NCBI Accession #U26943) wasprovided by D. M. Spencer, Baylor College of Medicine. A plasmidencoding human protein kinase R (#U50648) was from E. F. Meurs, InstitutPasteur. A plasmid encoding human RNase L (#CAA52920) was provided by R.Silverman, Cleveland Clinic Foundation. A plasmid encoding human Apaf-1(#NM_(—)013229, NM_(—)001160) was donated by Y. Shi, PrincetonUniversity. A plasmid encoding human BPI (#NM_(—)001725) was provided byL. J. Beamer, University of Missouri-Columbia. The mammalian expressionvector pTRE2hyg, 293 Tet-On™ human cell line, doxycycline, andtetracycline-free fetal bovine serum were obtained from BD BiosciencesClontech. The pCR®2.1-TOPO vector was supplied by Invitrogen. PCRprimers, Lipofectamine™ 2000 reagent, LIPOFECTIN® reagent, and PLUSreagent were obtained from Gibco BRL/Life Technologies/Invitrogen.Polyclonal goat IgG antibodies specific for human caspase 3 come fromR&D Systems. Polyclonal rabbit antibodies specific for human BPI werefrom Cell Sciences, Inc. Antibodies specific for human Apaf-1 were fromExalpha Biologicals (polyclonal rabbit IgG) and Santa Cruz Biotechnology(polyclonal goat IgG). Secondary anti-goat and anti-rabbit antibodieswere from Santa Cruz Biotechnology and Zymed.

Results and Discussion

FIG. 42 illustrates the synthesis strategy for PCR product 25, whichencodes a novel pathogen-activated caspase activator.2′,5′-oligoadenylate is produced within cells in response to pathogencomponents such as dsRNA. The 2′,5′-oligoadenylate-binding domain fromRNase L (amino acids 1-335) was fused in frame with a short flexiblepolypeptide linker (amino acid sequence S-G-G-G-S-G (SEQ ID NO: 1)) andamino acids 1-97 of Apaf-1, which included the caspase recruitmentdomain (CARD) that binds to procaspase 9. A Kozak sequence and stopcodon were included as shown. BamH I and Mlu I restriction sites wereincluded at the ends for ease of insertion into the pTRE2hyg vector. PCR21 used the indicated 5′ and 3′ PCR primers to copy the region encodingamino acids 1-335 of RNase L from the provided plasmid. PCR 22 used theindicated 5′ and 3′ PCR primers to copy the region encoding amino acids1-97 of Apaf-1 from the provided plasmid. PCR 25 used the gel-purifiedproducts of PCR 21 and 22, 5′ primer from PCR 21, and 3′ primer from PCR22 to create the desired product via splicing by overlap extension (C.W. Dieffenbach and G. S. Dveksler (eds.), PCR Primer: A LaboratoryManual, (1995), Cold Spring Harbor Laboratory Press, Plainview, N.Y.).

FIG. 43 illustrates the synthesis strategy for PCR product 26, whichencodes a novel pathogen-activated caspase activator. Lipopolysaccharide(LPS) is a component of pathogens such as bacteria. The LPS-bindingdomain from BPI (amino acids 1-199) was fused in frame with a shortflexible polypeptide linker (amino acid sequence S-G-G-G-S-G (SEQ ID NO:1)) and amino acids 1-97 of Apaf-1, which included the caspaserecruitment domain (CARD) that binds to procaspase 9. A Kozak sequenceand stop codon were included as shown. BamH I and Mlu I restrictionsites were included at the ends for ease of insertion into the pTRE2hygvector. PCR 23 used the indicated 5′ and 3′ PCR primers to copy theregion encoding amino acids 1-199 of BPI from the provided plasmid. PCR22 used the indicated 5′ and 3′ PCR primers to copy the region encodingamino acids 1-97 of Apaf-1 from the provided plasmid. PCR 26 used thegel-purified products of PCR 22 and 23, 5′ primer from PCR 23, and 3′primer from PCR 22 to create the desired product via splicing by overlapextension.

FIG. 44 illustrates the synthesis strategy for PCR product 27, whichencodes a novel dsRNA-activated caspase activator. The dsRNA-bindingdomain from PKR (amino acids 1-174) and part of the natural linkerregion from PKR (amino acids 175-181) were fused in frame with aminoacids 1-97 of Apaf-1, which included the caspase recruitment domain(CARD) that binds to procaspase 9. When two or more copies of theprotein encoded by PCR 27 are crosslinked by dsRNA, they will crosslinkand activate endogenous (pro)caspase 9. A Kozak sequence and stop codonwere included as shown. BamH I and Mlu I restriction sites were includedat the ends for ease of insertion into the pTRE2hyg vector. PCR 3 usedthe indicated 5′ and 3′ PCR primers to copy the region encoding aminoacids 1-181 of PKR from the provided plasmid. PCR 24 used the indicated5′ and 3′ PCR primers to copy the region encoding amino acids 1-97 ofApaf-1 from the provided plasmid. PCR 27 used the gel-purified productsof PCR 3 and 24, 5′ primer from PCR 3, and 3′ primer from PCR 24 tocreate the desired product via splicing by overlap extension.

FIG. 45 illustrates the synthesis strategy for PCR product 28, whichencodes a novel pathogen-activated caspase. 2′,5′-oligoadenylate isproduced within cells in response to pathogen components such as dsRNA.The 2′,5′-oligoadenylate-binding domain from RNase L (amino acids 1-335)was fused in frame with a short flexible polypeptide linker (amino acidsequence S-G-G-G-S-G (SEQ ID NO: 1)) and full-length caspase 3. A Kozaksequence and stop codon were included as shown. BamH I and Mlu Irestriction sites were included at the ends for ease of insertion intothe pTRE2hyg vector. PCR 21 used the indicated 5′ and 3′ PCR primers tocopy the region encoding amino acids 1-335 of RNase L from the providedplasmid. PCR 2 used the indicated 5′ and 3′ PCR primers to copy thecoding sequence of caspase 3 from the provided plasmid. PCR 28 used thegel-purified products of PCR 21 and 2, 5′ primer from PCR 21, and 3′primer from PCR 2 to create the desired product via splicing by overlapextension.

FIG. 46 illustrates the synthesis strategy for PCR product 29, whichencodes a novel pathogen-activated caspase. Lipopolysaccharide (LPS) isa component of pathogens such as bacteria. The LPS-binding domain fromBPI (amino acids 1-199) was fused in frame with a short flexiblepolypeptide linker (amino acid sequence S-G-G-G-S-G (SEQ ID NO: 1)) andfull-length caspase 3. A Kozak sequence and stop codon were included asshown. BamH I and Mlu I restriction sites were included at the ends forease of insertion into the pTRE2hyg vector. PCR 23 used the indicated 5′and 3′ PCR primers to copy the region encoding amino acids 1-199 of BPIfrom the provided plasmid. PCR 2 used the indicated 5′ and 3′ PCRprimers to copy the coding sequence of caspase 3 from the providedplasmid. PCR 29 used the gel-purified products of PCR 23 and 2, 5′primer from PCR 23, and 3′ primer from PCR 2 to create the desiredproduct via splicing by overlap extension.

PCR products 25, 26, 27, 28, and 29 were gel purified and inserted intothe Invitrogen pCR®2.1-TOPO vector following the manufacturer'sprotocol. The inserts were sequenced on both strands by the NucleicAcid/Protein Research Core Facility at the Children's Hospital ofPhiladelphia. The pCR®2.1-TOPO vectors containing PCR products 25through 29 were digested by BamH I and Mlu I restriction enzymes, andthe fragments corresponding to PCR products 25 through 29 were gelpurified. The pTRE2hyg vector, shown schematically in FIG. 47, was alsodigested by BamH I and Mlu I, and the larger resulting fragment was gelpurified. Then the digested PCR products 25 through 29 were ligated intothe digested vector to create expression vectors for PCR 25, 26, 27, 28,and 29. The vectors include a doxycycline or tetracycline-induciblepromoter for the inserted gene, as well as a hygromycin resistance genefor selection of transfected cells. The inserted region of the newvectors was sequenced on both strands by the Nucleic Acid/ProteinResearch Core Facility at the Children's Hospital of Philadelphia. Allof the vectors with the inserted genes were linearized for transfectionusing the Fsp I restriction enzyme and are shown in the DNA gelelectrophoresis photo in FIG. 47.

The 293 Tet-On™ human cell line contains the rtTA regulatory proteinnecessary for the proper functioning of the tetracycline ordoxycycline-inducible promoters. Cells were maintained using standardtissue culture practices, humidified incubators at 37° C. and 5% CO₂,and DMEM culture medium containing 10% tetracycline-free fetal bovineserum, 100 μM nonessential amino acids, 1 mM sodium pyruvate, 4 mML-glutamine, 100 units/ml penicillin G, 100 μg/ml streptomycin, 250ng/ml amphotericin B, and 100 μg/ml G418.

The linearized pTRE2hyg-derived vectors with inserted PCR 25, 26, 27,28, or 29 were transfected into the 293 Tet-On™ cells. The transfectionsuse Lipofectamine™ 2000 reagent from Invitrogen and follow Invitrogen'srecommended protocol for 293 cells. One day after the transfection, 200μg/ml hygromycin was added to the cell culture medium to kill any cellsthat had not been stably transfected with the vectors, and the cellswere permanently kept in this concentration of hygromycin as aprecaution against the possibility that the cells might lose thetransfected genes.

The pools of hygromycin-resistant cells that result from eachtransfection were presumably genetically heterogeneous, with differentcells having different copy numbers of the inserted vector or having thevector inserted into different regions of the cellular genome.Therefore, genetically homogeneous clonal cell populations wereisolated. Limiting dilutions of the pools of transfected cells were usedto deposit approximately 1 cell per well into 96-well plates, and thecells were allowed to multiply. Wells that appeared to have receivedmore than one initial cell were disregarded. The resulting clonal cellpopulations were designated 293 25-x, 26-x, 27-x, 28-x, or 29-x; thefirst number after the cell line name indicates which PCR product fromFIGS. 42-46 was transfected into the cells, and the x is replaced withthe cell clone number. For example, cell line 293 25-3 indicates PCRproduct 25, cell clone 3.

Western blots were used to analyze the cell clones. Antibodies listedabove in the Materials and Methods section were used to detect fusionproteins containing regions of caspase 3, Apaf-1, and/or BPI. Cells werecultured for two days either with or without doxycycline, and thenproteins were extracted from the cells and analyzed by Western blotfollowing the manufacturers' protocols.

Example 6

Anti-Pathogen Treatments that Involve Heat Shock Proteins, ImportInhibitors, or dsRNase

Plasmids encoding human importin α1 (NCBI Accession #NM_(—)002266),importin α4 (#NM_(—)002267), and importin α6 (#NM_(—)002269) wereprovided by B. R. Cullen, Duke University. A plasmid encodingEscherichia coli (E. coli) RNase III (#NP_(—)417062, NC_(—)000913) wasfrom A. W. Nicholson, Wayne State University. A plasmid encoding thehuman papillomavirus 16 (HPV-16) E5 protein (#W5WLHS) was provided by D.J. McCance, University of Rochester. A plasmid encoding the Salmonellaenterica SpiC protein (#U51927) was donated by E. A. Groisman,Washington University in St. Louis. Rat IgG₁ monoclonal antibodiesspecific for the hemagglutinin (HA) epitope were provided by Roche.Monoclonal mouse antibodies specific for human Hdj-1 (also known asHsp40) and human Hsp70 were from Stressgen. Rat antibodies specific forhuman Hsp90 were provided by Calbiochem. Secondary anti-mouse andanti-rat antibodies were from Santa Cruz Biotechnology and Zymed.

FIG. 52 illustrates the synthesis strategy for a truncated importin α1gene and its insertion into the pCMV/Bsd/ISRE vector described supra toproduce the new vector pCMV/Bsd/ISRE/α1. The region encoding amino acids100-529 of importin α1 was cloned from the provided plasmid using PCRwith the illustrated 3′ PCR primer and the first 5′ primer. Theresulting PCR product was gel purified and used in a subsequent PCR withthe same 3′ primer and the second 5′ primer. This final PCR productincludes Sal I and Mlu I restriction sites for ease of insertion into avector, a Kozak sequence and stop codon for translation, and an HAepitope for detection via immunoassays. It encodes a truncated versionof importin α1 that lacks the importin-β-binding domain. This PCRproduct was gel purified and inserted into the Invitrogen pCR®2.1-TOPOvector following the manufacturer's protocol. The insert was sequencedon both strands by the Nucleic Acid/Protein Research Core Facility atthe Children's Hospital of Philadelphia. The pCR®2.1-TOPO vectorcontaining the PCR insert was digested by Sal I and Mlu I restrictionenzymes, and the fragment corresponding to the PCR product was gelpurified. The pCMV/Bsd/ISRE vector was also digested by Sal I and Mlu I,and the larger resulting fragment was gel purified. Then the digestedPCR product was ligated into the digested vector to create theexpression vector pCMV/Bsd/ISRE/α1.

FIG. 53 is a schematic for the production of PCR product 30. PCR wascarried out using the illustrated PCR primers and the vectorpCMV/Bsd/ISRE/α1. The resulting PCR product 30 has Bam HI and Mlu Irestriction sites for ease of insertion into the pTRE2hyg vector. Itencodes a truncated form of importin α1 that lacks theimportin-β-binding domain but includes an HA epitope.

FIG. 54 illustrates the synthesis strategy for a truncated importin α4gene and its insertion into the pCMV/Bsd/ISRE vector described supra toproduce the new vector pCMV/Bsd/ISRE/α4. The region encoding amino acids95-521 of importin α4 was cloned from the provided plasmid using PCRwith the illustrated 3′ PCR primer and the first 5′ primer. Theresulting PCR product was gel purified and used in a subsequent PCR withthe same 3′ primer and the second 5′ primer. This final PCR productincludes Bss HII and Hind III restriction sites for ease of insertioninto a vector, a Kozak sequence and stop codon for translation, and anHA epitope for detection via immunoassays. It encodes a truncatedversion of importin α4 that lacks the importin-β-binding domain. ThisPCR product was gel purified and inserted into the InvitrogenpCR®2.1-TOPO vector following the manufacturer's protocol. The insertwas sequenced on both strands by the Nucleic Acid/Protein Research CoreFacility at the Children's Hospital of Philadelphia. The pCR®2.1-TOPOvector containing the PCR insert was digested by Bss HII and Hind IIIrestriction enzymes, and the fragment corresponding to the PCR productwas gel purified. The pCMV/Bsd/ISRE vector was also digested by Bss HIIand Hind III, and the larger resulting fragment was gel purified. Thenthe digested PCR product was ligated into the digested vector to createthe expression vector pCMV/Bsd/ISRE/α4.

FIG. 55 is a schematic for the production of PCR product 31. PCR wascarried out using the illustrated PCR primers and the vectorpCMV/Bsd/ISRE/α4. The resulting PCR product 31 has Mlu I and Not Irestriction sites for ease of insertion into the pTRE2hyg vector. Itencodes a truncated form of importin α4 that lacks theimportin-β-binding domain but includes an HA epitope.

FIG. 56 illustrates the synthesis strategy for a truncated importin α6gene and its insertion into the pCMV/Bsd/ISRE vector described supra toproduce the new vector pCMV/Bsd/ISRE/α6. The region encoding amino acids104-536 of importin α1 was cloned from the provided plasmid using PCRwith the illustrated 3′ PCR primer and the first 5′ primer. Theresulting PCR product was gel purified and used in a subsequent PCR withthe same 3′ primer and the second 5′ primer. This final PCR productincludes Bss HII and Hind III restriction sites for ease of insertioninto a vector, a Kozak sequence and stop codon for translation, and anHA epitope for detection via immunoassays. It encodes a truncatedversion of importin α6 that lacks the importin-β-binding domain. ThisPCR product was gel purified and inserted into the InvitrogenpCR®2.1-TOPO vector following the manufacturer's protocol. The insertwas sequenced on both strands by the Nucleic Acid/Protein Research CoreFacility at the Children's Hospital of Philadelphia. The pCR®2.1-TOPOvector containing the PCR insert was digested by Bss HII and Hind IIIrestriction enzymes, and the fragment corresponding to the PCR productwas gel purified. The pCMV/Bsd/ISRE vector was also digested by Bss HIIand Hind III, and the larger resulting fragment was gel purified. Thenthe digested PCR product was ligated into the digested vector to createthe expression vector pCMV/Bsd/ISRE/α6.

FIG. 57 is a schematic for the production of PCR product 32. PCR wascarried out using the illustrated PCR primers and the vectorpCMV/Bsd/ISRE/α6. The resulting PCR product 32 has Bam HI and Mlu Irestriction sites for ease of insertion into the pTRE2hyg vector. Itencodes a truncated form of importin α6 that lacks theimportin-β-binding domain but includes an HA epitope.

FIG. 58 illustrates the creation of a gene encoding E. coli RNase IIIwith an HA epitope, and its subsequent insertion into the pCMV/Bsd/ISREvector described supra to produce the new vector pCMV/Bsd/ISRE/RNaseIII. The region encoding full-length RNase III was cloned from theprovided plasmid using PCR with the illustrated 3′ PCR primer and thefirst 5′ primer. The resulting PCR product was gel purified and used ina subsequent PCR with the same 3′ primer and the second 5′ primer. Thisfinal PCR product includes Sal I and Mlu I restriction sites for ease ofinsertion into a vector, a Kozak sequence and stop codon fortranslation, and an HA epitope for detection via immunoassays. This PCRproduct was gel purified and inserted into the Invitrogen pCR®2.1-TOPOvector following the manufacturer's protocol. The insert was sequencedon both strands by the Nucleic Acid/Protein Research Core Facility atthe Children's Hospital of Philadelphia. The pCR®2.1-TOPO vectorcontaining the PCR insert was digested by Sal I and Mlu I restrictionenzymes, and the fragment corresponding to the PCR product was gelpurified. The pCMV/Bsd/ISRE vector was also digested by Sal I and Mlu I,and the larger resulting fragment was gel purified. Then the digestedPCR product was ligated into the digested vector to create theexpression vector pCMV/Bsd/ISRE/RNase III.

FIG. 59 is a schematic for the production of PCR product 33. PCR wascarried out using the illustrated PCR primers and the vectorpCMV/Bsd/ISRE/RNase III. The resulting PCR product 33 has Bam HI and MluI restriction sites for ease of insertion into the pTRE2hyg vector. Itencodes E. coli RNase III with an HA epitope.

FIG. 60 is a schematic for the insertion of a gene encoding the HPV-16E5 protein into the pCMV/Bsd/ISRE vector described supra to produce thenew vector pCMV/Bsd/ISRE/E5. The region encoding full-length RNase IIIwas cloned from the provided plasmid using PCR with the illustrated 5′and 3′ PCR primers. The PCR product includes Bss HII and Hind IIIrestriction sites for ease of insertion into a vector, and a Kozaksequence and stop codon for translation. This PCR product was gelpurified and inserted into the Invitrogen pCR®2.1-TOPO vector followingthe manufacturer's protocol. The insert was sequenced on both strands bythe Nucleic Acid/Protein Research Core Facility at the Children'sHospital of Philadelphia. The pCR®2.1-TOPO vector containing the PCRinsert was digested by Bss HII and Hind III restriction enzymes, and thefragment corresponding to the PCR product was gel purified. ThepCMV/Bsd/ISRE vector was also digested by Bss HII and Hind III, and thelarger resulting fragment was gel purified. Then the digested PCRproduct was ligated into the digested vector to create the expressionvector pCMV/Bsd/ISRE/E5.

FIG. 61 is a schematic for the production of PCR product 34. PCR wascarried out using the illustrated PCR primers and the vectorpCMV/Bsd/ISRE/E5. The resulting PCR product 34 has Bam HI and Mlu Irestriction sites for ease of insertion into the pTRE2hyg vector. Itencodes the HPV-16 E5 protein.

FIG. 62 illustrates the synthesis strategy for a gene encoding theSalmonella SpiC protein with an HA epitope, and its subsequent insertioninto the pCMV/Bsd/ISRE vector described supra to produce the new vectorpCMV/Bsd/ISRE/SpiC. The region encoding full-length SpiC was cloned fromthe provided plasmid using PCR with the illustrated 3′ PCR primer andthe first 5′ primer. The resulting PCR product was gel purified and usedin a subsequent PCR with the same 3′ primer and the second 5′ primer.This final PCR product includes Sal I and Mlu I restriction sites forease of insertion into a vector, a Kozak sequence and stop codon fortranslation, and an HA epitope for detection via immunoassays. This PCRproduct was gel purified and inserted into the Invitrogen pCR®2.1-TOPOvector following the manufacturer's protocol. The insert was sequencedon both strands by the Nucleic Acid/Protein Research Core Facility atthe Children's Hospital of Philadelphia. The pCR®2.1-TOPO vectorcontaining the PCR insert was digested by Sal I and Mlu I restrictionenzymes, and the fragment corresponding to the PCR product was gelpurified. The pCMV/Bsd/ISRE vector was also digested by Sal I and Mlu I,and the larger resulting fragment was gel purified. Then the digestedPCR product was ligated into the digested vector to create theexpression vector pCMV/Bsd/ISRE/SpiC.

FIG. 63 is a schematic for the production of PCR product 35. PCR wascarried out using the illustrated PCR primers and the vectorpCMV/Bsd/ISRE/SpiC. The resulting PCR product 35 has Bam HI and Mlu Irestriction sites for ease of insertion into the pTRE2hyg vector. Itencodes the Salmonella SpiC protein with an HA epitope.

FIG. 64 is a schematic for the production of PCR product 36. PCR wascarried out using the illustrated PCR primers and the vectorpCMV/Bsd/ISRE/Hdj 1. The resulting PCR product 36 has Bam HI and Mlu Irestriction sites for ease of insertion into the pTRE2hyg vector. Itencodes human Hdj-1, also known as Hsp40.

FIG. 65 is a schematic for the production of PCR product 37. PCR wascarried out using the illustrated PCR primers and the vectorpCMV/Bsd/ISRE/Hsp70. The resulting PCR product 37 has Bam HI and Mlu Irestriction sites for ease of insertion into the pTRE2hyg vector. Itencodes human Hsp70.

FIG. 66 is a schematic for the production of PCR product 38. PCR wascarried out using the illustrated PCR primers and the vectorpCMV/Bsd/ISRE/Hsp90. The resulting PCR product 38 has Mlu I and Not Irestriction sites for ease of insertion into the pTRE2hyg vector. Itencodes human Hsp90.

PCR products 30, 31, 32, 33, 34, 35, 36, 37, and 38 were gel purifiedand inserted into the Invitrogen pCR®2.1-TOPO vector following themanufacturer's protocol. The inserts were sequenced on both strands bythe Nucleic Acid/Protein Research Core Facility at the Children'sHospital of Philadelphia.

The pCR®2.1-TOPO vectors containing PCR products 30, 32, 33, 34, 35, 36,and 37 were digested by BamH I and Mlu I restriction enzymes, and thefragments corresponding to the PCR products were gel purified. ThepTRE2hyg vector was also digested by BamH I and Mlu I, and the largerresulting fragment was gel purified. Then the digested PCR products wereligated into the digested vector to create expression vectors for PCR30, 32, 33, 34, 35, 36, and 37.

The pCR®2.1-TOPO vectors containing PCR products 31 and 38 were digestedby Mlu I and Not I restriction enzymes, and the fragments correspondingto the PCR products were gel purified. The pTRE2hyg vector was alsodigested by Mlu I and Not I, and the larger resulting fragment was gelpurified. Then the digested PCR products were ligated into the digestedvector to create expression vectors for PCR 31 and 38.

The expression vectors include a doxycycline or tetracycline-induciblepromoter for the inserted gene, as well as a hygromycin resistance genefor selection of transfected cells. The inserted region of the newvectors was sequenced on both strands by the Nucleic Acid/ProteinResearch Core Facility at the Children's Hospital of Philadelphia. Allof the vectors with the inserted genes were linearized for transfectionusing the Fsp I restriction enzyme (except the vector with PCR 37, whichwas linearized with Apa I) and purified with the Zymo Research DNA Clean& Concentrator kit. The prepared vectors are shown in the DNA gelelectrophoresis photo in FIG. 67.

The 293 Tet-On™ human cell line contains the rtTA regulatory proteinnecessary for the proper functioning of the tetracycline ordoxycycline-inducible promoters. Cells were maintained using standardtissue culture practices, humidified incubators at 37° C. and 5% CO₂,and DMEM culture medium containing 10% tetracycline-free fetal bovineserum, 100 μM nonessential amino acids, 1 mM sodium pyruvate, 4 mML-glutamine, 100 units/ml penicillin G, 100 μg/ml streptomycin, 250ng/ml amphotericin B, and 100 μg/ml G418.

The linearized pTRE2hyg-derived vectors with inserted PCR 30, 31, 32,33, 34, 35, 36, 37, or 38 were transfected into the 293 Tet-On™ cells.The transfections use Lipofectamine™ 2000 reagent from Invitrogen andfollow Invitrogen's recommended protocol for 293 cells. One day afterthe transfection, 200 μg/ml hygromycin was added to the cell culturemedium to kill any cells that have not been stably transfected with thevectors, and the cells were permanently kept in this concentration ofhygromycin as a precaution against the possibility that the cells mightlose the transfected genes.

The pools of hygromycin-resistant cells that result from each of thesetransfections were presumably genetically heterogeneous, with differentcells having different copy numbers of the inserted vector or having thevector inserted into different regions of the cellular genome.Therefore, genetically homogeneous clonal cell populations wereisolated. Limiting dilutions of the pools of transfected cells were usedto deposit approximately 1 cell per well into 96-well plates, and thecells were allowed to multiply. Wells that appear to have received morethan one initial cell were disregarded. The resulting clonal cellpopulations were designated 293 30-x, 31-x, 32-x, 33-x, 34-x, 35-x,36-x, 37-x, or 38-x; the first number indicates which PCR product wastransfected into the cells, and the x is replaced with the cell clonenumber. For example, cell line 293 30-3 indicates PCR product 30, cellclone 3.

H1-HeLa cells were maintained using standard tissue culture practices,humidified incubators at 37° C. and 5% CO₂, and DMEM culture mediumcontaining 10% fetal bovine serum, 100 μM nonessential amino acids, 1 mMsodium pyruvate, 4 mM L-glutamine, 100 units/ml penicillin G, 100 μg/mlstreptomycin, and 250 ng/ml amphotericin B.

The new expression vectors derived from pCMV/Bsd/ISRE were linearizedwith the Apa I restriction enzyme, purified with the Zymo Research DNAClean & Concentrator kit, and transfected into the H1-HeLa cells. Thetransfections use LIPOFECTIN® and PLUS reagents from Invitrogen andfollow Invitrogen's recommended protocol for HeLa cells. One day afterthe transfection, 4 μg/ml blasticidin was added to the cell culturemedium to kill any cells that have not been stably transfected with thevectors, and the cells were permanently kept in blasticidin as aprecaution against the possibility that the cells might lose thetransfected genes.

The pools of blasticidin-resistant cells that result from each of thesetransfections were presumably genetically heterogeneous, with differentcells having different copy numbers of the inserted vector or having thevector inserted into different regions of the cellular genome.Therefore, genetically homogeneous clonal cell populations wereisolated. Limiting dilutions of the pools of transfected cells were usedto deposit approximately 1 cell per well into 96-well plates, and thecells were allowed to multiply. Wells that appear to have received morethan one initial cell were disregarded.

Example 7

Production and Testing of Anti-Pathogen Proteins that can be Transducedinto Cells In Vitro or In Vivo

Materials

The vector pET100/D-TOPO®, E. coli strain BL21(DE)pLysS, Ni-NTApurification kit with anti-Xpress™ antibodies, EKMax™ enterokinase, andEK-Away™ resin are obtained from Invitrogen. The vector pCMV.IRES.AEQwas provided by D. Button, Stanford University, and the vectorpEGFP-IRES-puro is from Clontech.

Methods

FIG. 68 illustrates schematically how to produce test proteins thatcontain protein transduction domains or tags. The tag can have an aminoacid sequence such as one of those shown from HIV TAT (S. R. Schwarze,K. A. Hruska, and S. F. Dowdy (2000) Trends in Cell Biology 10,290-295), PTD-4 (A. Ho et al. (2001) Cancer Research 61, 474-477), anarginine-rich sequence (P. A. Wender et al. (2000) Proc. Natl. Acad.Sci. 97, 13003-13008; J. B. Rothbard et al. (2002) J. Med. Chem. 45,3612-3618), or any other amino acid sequence that facilitates uptakeand/or targeting to cells in vitro or in vivo. The encoded test proteincan have anti-pathogen effects or be any other protein or amino acidsequence. The PTD sequence is fused in frame at either end of the testprotein or within the test protein. The DNA sequence encoding the fusedPTD and test protein is inserted into an expression vector. Theillustrated vector is a prokaryotic vector, but an expression vector foryeast, insect cells, mammalian cells, in vitro transcription andtranslation systems, or other protein expression system can be used. Anysuitable prokaryotic expression vector can be used; the exampleillustrated is the Invitrogen pET100/D-TOPO® vector, which encodes asix-histidine tag for protein purification, Xpress™ epitope forimmunoassays, and enterokinase site for cleavage.

The expression vector is transformed into a suitable expression system,as will be understood by one of skill in the art, which in theillustrated example is the E. coli strain BL21(DE)pLysS. Afterapproximately 6-24 hours, the tagged expressed protein is harvested fromthe expression system using the Invitrogen Ni-NTA purification kit andfollowing either the manufacturer's directions or the protocol in M.Becker-Hapak, S. S. McAllister, and S. F. Dowdy (2001) Methods 24,247-256. Protocols for either denatured protein or soluble proteinproduct can be followed. If desired, Invitrogen EKMax™ enterokinase andEK-Away™ resin are used as per the manufacturer's directions to removethe six-histidine and Xpress™ tags and re-purify the protein.

FIG. 69 illustrates PCR primers for producing a DNA sequence encodingaequorin fused to one of the following protein transduction tags: TAT,PTD-4, an arginine-rich sequence Arg, or no protein transduction tag.Glycine residues are included at the ends of the protein transductiontags to permit rotation or flexing of the resulting amino acid sequenceat those points. For a TAT tag, a first PCR is carried out with thefirst 5′ TAT primer, the 3′ primer, and the vector pCMV.IRES.AEQ; theresulting PCR product is gel purified and used in a second PCR with thesecond 5′ TAT primer and the 3′ primer. This PCR product is gel purifiedand inserted into the pET100/D-TOPO® vector following the manufacturer'sdirections. For a PTD-4 tag, a first PCR is carried out with the first5′ PTD-4 primer, the 3′ primer, and the vector pCMV.IRES.AEQ; theresulting PCR product is gel purified and used in a second PCR with thesecond 5′ PTD-4 primer and the 3′ primer. This PCR product is gelpurified and inserted into the pET100/D-TOPO® vector following themanufacturer's directions. For an Arg tag, a first PCR is carried outwith the first 5′ Arg primer, the 3′ primer, and the vectorpCMV.IRES.AEQ; the resulting PCR product is gel purified and used in asecond PCR with the second 5′ Arg primer and the 3′ primer. This PCRproduct is gel purified and inserted into the pET100/D-TOPO® vectorfollowing the manufacturer's directions. For no protein transductiontag, a PCR is carried out with the 5′ primer for no tag, the 3′ primer,and the vector pCMV.IRES.AEQ; the resulting PCR product is gel purifiedand inserted into the pET100/D-TOPO® vector following the manufacturer'sdirections. The inserts in pET100/D-TOPO® are sequenced on both strandsfor sequence confirmation. Transducible aequorin is used to evaluate therelative efficiencies of the protein transduction tags.

FIG. 70 illustrates PCR primers for producing a DNA sequence encodingenhanced green fluorescent protein (EGFP) fused to one of the followingprotein transduction tags: TAT, PTD-4, an arginine-rich sequence Arg, orno protein transduction tag. Glycine residues are included at the endsof the protein transduction tags to permit rotation or flexing of theresulting amino acid sequence at those points. For a TAT tag, a firstPCR is carried out with the first 5′ TAT primer, the 3′ primer, and thevector pEGFP-IRES-puro; the resulting PCR product is gel purified andused in a second PCR with the second 5′ TAT primer and the 3′ primer.This PCR product is gel purified and inserted into the pET100/D-TOPO®vector following the manufacturer's directions. For a PTD-4 tag, a firstPCR is carried out with the first 5′ PTD-4 primer, the 3′ primer, andthe vector pEGFP-IRES-puro; the resulting PCR product is gel purifiedand used in a second PCR with the second 5′ PTD-4 primer and the 3′primer. This PCR product is gel purified and inserted into thepET100/D-TOPO® vector following the manufacturer's directions. For anArg tag, a first PCR is carried out with the first 5′ Arg primer, the 3′primer, and the vector pEGFP-IRES-puro; the resulting PCR product is gelpurified and used in a second PCR with the second 5′ Arg primer and the3′ primer. This PCR product is gel purified and inserted into thepET100/D-TOPO® vector following the manufacturer's directions. For noprotein transduction tag, a PCR is carried out with the 5′ primer for notag, the 3′ primer, and the vector pEGFP-IRES-puro; the resulting PCRproduct is gel purified and inserted into the pET100/D-TOPO® vectorfollowing the manufacturer's directions. The inserts in pET100/D-TOPO®are sequenced on both strands for sequence confirmation. TransducibleEGFP is used to evaluate the relative efficiencies of the proteintransduction tags.

FIG. 71 illustrates PCR primers for producing a DNA sequence thatincludes the coding sequence from PCR product 7 or 8 fused to one of thefollowing protein transduction tags: TAT, PTD-4, an arginine-richsequence Arg, or no protein transduction tag. Glycine residues areincluded at the ends of the protein transduction tags to permit rotationor flexing of the resulting amino acid sequence at those points. For aTAT tag, a first PCR is carried out with the first 5′ TAT primer, the 3′primer, and gel-purified PCR product 7 or 8 or a vector that contains ofone of them; the resulting PCR product is gel purified and used in asecond PCR with the second 5′ TAT primer and the 3′ primer. This PCRproduct is gel purified and inserted into the pET100/D-TOPO® vectorfollowing the manufacturer's directions. For a PTD-4 tag, a first PCR iscarried out with the first 5′ PTD-4 primer, the 3′ primer, andgel-purified PCR product 7 or 8 or a vector that contains of one ofthem; the resulting PCR product is gel purified and used in a second PCRwith the second 5′ PTD-4 primer and the 3′ primer. This PCR product isgel purified and inserted into the pET100/D-TOPO® vector following themanufacturer's directions. For an Arg tag, a first PCR is carried outwith the first 5′ Arg primer, the 3′ primer, and gel-purified PCRproduct 7 or 8 or a vector that contains of one of them; the resultingPCR product is gel purified and used in a second PCR with the second 5′Arg primer and the 3′ primer. This PCR product is gel purified andinserted into the pET100/D-TOPO® vector following the manufacturer'sdirections. For no protein transduction tag, a PCR is carried out withthe 5′ primer for no tag, the 3′ primer, and gel-purified PCR product 7or 8 or a vector that contains of one of them; the resulting PCR productis gel purified and inserted into the pET100/D-TOPO® vector followingthe manufacturer's directions. The inserts in pET100/D-TOPO® aresequenced on both strands for sequence confirmation.

FIG. 72 illustrates PCR primers for producing a DNA sequence thatincludes the coding sequence from PCR product 9 or 10 fused to one ofthe following protein transduction tags: TAT, PTD-4, an arginine-richsequence Arg, or no protein transduction tag. Glycine residues areincluded at the ends of the protein transduction tags to permit rotationor flexing of the resulting amino acid sequence at those points. For aTAT tag, a first PCR is carried out with the first 5′ TAT primer, the 3′primer, and gel-purified PCR product 9 or 10 or a vector that containsof one of them; the resulting PCR product is gel purified and used in asecond PCR with the second 5′ TAT primer and the 3′ primer. This PCRproduct is gel purified and inserted into the pET100/D-TOPO® vectorfollowing the manufacturer's directions. For a PTD-4 tag, a first PCR iscarried out with the first 5′ PTD-4 primer, the 3′ primer, andgel-purified PCR product 9 or 10 or a vector that contains of one ofthem; the resulting PCR product is gel purified and used in a second PCRwith the second 5′ PTD-4 primer and the 3′ primer. This PCR product isgel purified and inserted into the pET100/D-TOPO® vector following themanufacturer's directions. For an Arg tag, a first PCR is carried outwith the first 5′ Arg primer, the 3′ primer, and gel-purified PCRproduct 9 or 10 or a vector that contains of one of them; the resultingPCR product is gel purified and used in a second PCR with the second 5′Arg primer and the 3′ primer. This PCR product is gel purified andinserted into the pET100/D-TOPO® vector following the manufacturer'sdirections. For no protein transduction tag, a PCR is carried out withthe 5′ primer for no tag, the 3′ primer, and gel-purified PCR product 9or 10 or a vector that contains of one of them; the resulting PCRproduct is gel purified and inserted into the pET100/D-TOPO® vectorfollowing the manufacturer's directions. The inserts in pET100/D-TOPO®are sequenced on both strands for sequence confirmation.

FIG. 73 illustrates PCR primers for producing a DNA sequence thatincludes the coding sequence from PCR product 25 fused to one of thefollowing protein transduction tags: TAT, PTD-4, an arginine-richsequence Arg, or no protein transduction tag. Glycine residues areincluded at the ends of the protein transduction tags to permit rotationor flexing of the resulting amino acid sequence at those points. For aTAT tag, a first PCR is carried out with the first 5′ TAT primer, the 3′primer, and gel-purified PCR product 25 or a vector that contains thatPCR product; the resulting PCR product is gel purified and used in asecond PCR with the second 5′ TAT primer and the 3′ primer. This PCRproduct is gel purified and inserted into the pET100/D-TOPO® vectorfollowing the manufacturer's directions. For a PTD-4 tag, a first PCR iscarried out with the first 5′ PTD-4 primer, the 3′ primer, andgel-purified PCR product 25 or a vector that contains that PCR product;the resulting PCR product is gel purified and used in a second PCR withthe second 5′ PTD-4 primer and the 3′ primer. This PCR product is gelpurified and inserted into the pET100/D-TOPO® vector following themanufacturer's directions. For an Arg tag, a first PCR is carried outwith the first 5′ Arg primer, the 3′ primer, and gel-purified PCRproduct 25 or a vector that contains that PCR product; the resulting PCRproduct is gel purified and used in a second PCR with the second 5′ Argprimer and the 3′ primer. This PCR product is gel purified and insertedinto the pET100/D-TOPO® vector following the manufacturer's directions.For no protein transduction tag, a PCR is carried out with the 5′ primerfor no tag, the 3′ primer, and gel-purified PCR product 25 or a vectorthat contains that PCR product; the resulting PCR product is gelpurified and inserted into the pET100/D-TOPO® vector following themanufacturer's directions. The inserts in pET100/D-TOPO® are sequencedon both strands for sequence confirmation.

FIG. 74 illustrates PCR primers for producing a DNA sequence thatincludes the coding sequence from PCR product 26 fused to one of thefollowing protein transduction tags: TAT, PTD-4, an arginine-richsequence Arg, or no protein transduction tag. Glycine residues areincluded at the ends of the protein transduction tags to permit rotationor flexing of the resulting amino acid sequence at those points. For aTAT tag, a first PCR is carried out with the first 5′ TAT primer, the 3′primer, and gel-purified PCR product 26 or a vector that contains thatPCR product; the resulting PCR product is gel purified and used in asecond PCR with the second 5′ TAT primer and the 3′ primer. This PCRproduct is gel purified and inserted into the pET100/D-TOPO® vectorfollowing the manufacturer's directions. For a PTD-4 tag, a first PCR iscarried out with the first 5′ PTD-4 primer, the 3′ primer, andgel-purified PCR product 26 or a vector that contains that PCR product;the resulting PCR product is gel purified and used in a second PCR withthe second 5′ PTD-4 primer and the 3′ primer. This PCR product is gelpurified and inserted into the pET100/D-TOPO® vector following themanufacturer's directions. For an Arg tag, a first PCR is carried outwith the first 5′ Arg primer, the 3′ primer, and gel-purified PCRproduct 26 or a vector that contains that PCR product; the resulting PCRproduct is gel purified and used in a second PCR with the second 5′ Argprimer and the 3′ primer. This PCR product is gel purified and insertedinto the pET100/D-TOPO® vector following the manufacturer's directions.For no protein transduction tag, a PCR is carried out with the 5′ primerfor no tag, the 3′ primer, and gel-purified PCR product 26 or a vectorthat contains that PCR product; the resulting PCR product is gelpurified and inserted into the pET100/D-TOPO® vector following themanufacturer's directions. The inserts in pET100/D-TOPO® are sequencedon both strands for sequence confirmation.

FIG. 75 illustrates PCR primers for producing a DNA sequence thatincludes the coding sequence from PCR product 27 fused to one of thefollowing protein transduction tags: TAT, PTD-4, an arginine-richsequence Arg, or no protein transduction tag. Glycine residues areincluded at the ends of the protein transduction tags to permit rotationor flexing of the resulting amino acid sequence at those points. For aTAT tag, a first PCR is carried out with the first 5′ TAT primer, the 3′primer, and gel-purified PCR product 27 or a vector that contains thatPCR product; the resulting PCR product is gel purified and used in asecond PCR with the second 5′ TAT primer and the 3′ primer. This PCRproduct is gel purified and inserted into the pET100/D-TOPO® vectorfollowing the manufacturer's directions. For a PTD-4 tag, a first PCR iscarried out with the first 5′ PTD-4 primer, the 3′ primer, andgel-purified PCR product 27 or a vector that contains that PCR product;the resulting PCR product is gel purified and used in a second PCR withthe second 5′ PTD-4 primer and the 3′ primer. This PCR product is gelpurified and inserted into the pET100/D-TOPO® vector following themanufacturer's directions. For an Arg tag, a first PCR is carried outwith the first 5′ Arg primer, the 3′ primer, and gel-purified PCRproduct 27 or a vector that contains that PCR product; the resulting PCRproduct is gel purified and used in a second PCR with the second 5′ Argprimer and the 3′ primer. This PCR product is gel purified and insertedinto the pET100/D-TOPO® vector following the manufacturer's directions.For no protein transduction tag, a PCR is carried out with the 5′ primerfor no tag, the 3′ primer, and gel-purified PCR product 27 or a vectorthat contains that PCR product; the resulting PCR product is gelpurified and inserted into the pET100/D-TOPO® vector following themanufacturer's directions. The inserts in pET100/D-TOPO® are sequencedon both strands for sequence confirmation.

FIG. 76 illustrates PCR primers for producing a DNA sequence thatincludes the coding sequence from PCR product 28 fused to one of thefollowing protein transduction tags: TAT, PTD-4, an arginine-richsequence Arg, or no protein transduction tag. Glycine residues areincluded at the ends of the protein transduction tags to permit rotationor flexing of the resulting amino acid sequence at those points. For aTAT tag, a first PCR is carried out with the first 5′ TAT primer, the 3′primer, and gel-purified PCR product 28 or a vector that contains thatPCR product; the resulting PCR product is gel purified and used in asecond PCR with the second 5′ TAT primer and the 3′ primer. This PCRproduct is gel purified and inserted into the pET100/D-TOPO® vectorfollowing the manufacturer's directions. For a PTD-4 tag, a first PCR iscarried out with the first 5′ PTD-4 primer, the 3′ primer, andgel-purified PCR product 28 or a vector that contains that PCR product;the resulting PCR product is gel purified and used in a second PCR withthe second 5′ PTD-4 primer and the 3′ primer. This PCR product is gelpurified and inserted into the pET100/D-TOPO® vector following themanufacturer's directions. For an Arg tag, a first PCR is carried outwith the first 5′ Arg primer, the 3′ primer, and gel-purified PCRproduct 28 or a vector that contains that PCR product; the resulting PCRproduct is gel purified and used in a second PCR with the second 5′ Argprimer and the 3′ primer. This PCR product is gel purified and insertedinto the pET100/D-TOPO® vector following the manufacturer's directions.For no protein transduction tag, a PCR is carried out with the 5′ primerfor no tag, the 3′ primer, and gel-purified PCR product 28 or a vectorthat contains that PCR product; the resulting PCR product is gelpurified and inserted into the pET100/D-TOPO® vector following themanufacturer's directions. The inserts in pET100/D-TOPO® are sequencedon both strands for sequence confirmation.

FIG. 77 illustrates PCR primers for producing a DNA sequence thatincludes the coding sequence from PCR product 29 fused to one of thefollowing protein transduction tags: TAT, PTD-4, an arginine-richsequence Arg, or no protein transduction tag. Glycine residues areincluded at the ends of the protein transduction tags to permit rotationor flexing of the resulting amino acid sequence at those points. For aTAT tag, a first PCR is carried out with the first 5′ TAT primer, the 3′primer, and gel-purified PCR product 29 or a vector that contains thatPCR product; the resulting PCR product is gel purified and used in asecond PCR with the second 5′ TAT primer and the 3′ primer. This PCRproduct is gel purified and inserted into the pET100/D-TOPO® vectorfollowing the manufacturer's directions. For a PTD-4 tag, a first PCR iscarried out with the first 5′ PTD-4 primer, the 3′ primer, andgel-purified PCR product 29 or a vector that contains that PCR product;the resulting PCR product is gel purified and used in a second PCR withthe second 5′ PTD-4 primer and the 3′ primer. This PCR product is gelpurified and inserted into the pET100/D-TOPO® vector following themanufacturer's directions. For an Arg tag, a first PCR is carried outwith the first 5′ Arg primer, the 3′ primer, and gel-purified PCRproduct 29 or a vector that contains that PCR product; the resulting PCRproduct is gel purified and used in a second PCR with the second 5′ Argprimer and the 3′ primer. This PCR product is gel purified and insertedinto the pET100/D-TOPO® vector following the manufacturer's directions.For no protein transduction tag, a PCR is carried out with the 5′ primerfor no tag, the 3′ primer, and gel-purified PCR product 29 or a vectorthat contains that PCR product; the resulting PCR product is gelpurified and inserted into the pET100/D-TOPO® vector following themanufacturer's directions. The inserts in pET100/D-TOPO® are sequencedon both strands for sequence confirmation.

FIG. 78 illustrates PCR primers for producing a DNA sequence thatincludes the coding sequence from PCR product 30 fused to one of thefollowing protein transduction tags: TAT, PTD-4, an arginine-richsequence Arg, or no protein transduction tag. Glycine residues areincluded at the ends of the protein transduction tags to permit rotationor flexing of the resulting amino acid sequence at those points. For aTAT tag, a first PCR is carried out with the first 5′ TAT primer, the 3′primer, and gel-purified PCR product 30 or a vector that contains thatPCR product; the resulting PCR product is gel purified and used in asecond PCR with the second 5′ TAT primer and the 3′ primer. This PCRproduct is gel purified and inserted into the pET100/D-TOPO® vectorfollowing the manufacturer's directions. For a PTD-4 tag, a first PCR iscarried out with the first 5′ PTD-4 primer, the 3′ primer, andgel-purified PCR product 30 or a vector that contains that PCR product;the resulting PCR product is gel purified and used in a second PCR withthe second 5′ PTD-4 primer and the 3′ primer. This PCR product is gelpurified and inserted into the pET100/D-TOPO® vector following themanufacturer's directions. For an Arg tag, a first PCR is carried outwith the first 5′ Arg primer, the 3′ primer, and gel-purified PCRproduct 30 or a vector that contains that PCR product; the resulting PCRproduct is gel purified and used in a second PCR with the second 5′ Argprimer and the 3′ primer. This PCR product is gel purified and insertedinto the pET100/D-TOPO®; vector following the manufacturer's directions.For no protein transduction tag, a PCR is carried out with the 5′ primerfor no tag, the 3′ primer, and gel-purified PCR product 30 or a vectorthat contains that PCR product; the resulting PCR product is gelpurified and inserted into the pET100/D-TOPO® vector following themanufacturer's directions. The inserts in pET100/D-TOPO® are sequencedon both strands for sequence confirmation.

FIG. 79 illustrates PCR primers for producing a DNA sequence thatincludes the coding sequence from PCR product 31 fused to one of thefollowing protein transduction tags: TAT, PTD-4, an arginine-richsequence Arg, or no protein transduction tag. Glycine residues areincluded at the ends of the protein transduction tags to permit rotationor flexing of the resulting amino acid sequence at those points. For aTAT tag, a first PCR is carried out with the first 5′ TAT primer, the 3′primer, and gel-purified PCR product 31 or a vector that contains thatPCR product; the resulting PCR product is gel purified and used in asecond PCR with the second 5′ TAT primer and the 3′ primer. This PCRproduct is gel purified and inserted into the pET100/D-TOPO® vectorfollowing the manufacturer's directions. For a PTD-4 tag, a first PCR iscarried out with the first 5′ PTD-4 primer, the 3′ primer, andgel-purified PCR product 31 or a vector that contains that PCR product;the resulting PCR product is gel purified and used in a second PCR withthe second 5′ PTD-4 primer and the 3′ primer. This PCR product is gelpurified and inserted into the pET100/D-TOPO® vector following themanufacturer's directions. For an Arg tag, a first PCR is carried outwith the first 5′ Arg primer, the 3′ primer, and gel-purified PCRproduct 31 or a vector that contains that PCR product; the resulting PCRproduct is gel purified and used in a second PCR with the second 5′ Argprimer and the 3′ primer. This PCR product is gel purified and insertedinto the pET100/D-TOPO® vector following the manufacturer's directions.For no protein transduction tag, a PCR is carried out with the 5′ primerfor no tag, the 3′ primer, and gel-purified PCR product 31 or a vectorthat contains that PCR product; the resulting PCR product is gelpurified and inserted into the pET100/D-TOPO® vector following themanufacturer's directions. The inserts in pET100/D-TOPO® are sequencedon both strands for sequence confirmation.

FIG. 80 illustrates PCR primers for producing a DNA sequence thatincludes the coding sequence from PCR product 32 fused to one of thefollowing protein transduction tags: TAT, PTD-4, an arginine-richsequence Arg, or no protein transduction tag. Glycine residues areincluded at the ends of the protein transduction tags to permit rotationor flexing of the resulting amino acid sequence at those points. For aTAT tag, a first PCR is carried out with the first 5′ TAT primer, the 3′primer, and gel-purified PCR product 32 or a vector that contains thatPCR product; the resulting PCR product is gel purified and used in asecond PCR with the second 5′ TAT primer and the 3′ primer. This PCRproduct is gel purified and inserted into the pET100/D-TOPO® vectorfollowing the manufacturer's directions. For a PTD-4 tag, a first PCR iscarried out with the first 5′ PTD-4 primer, the 3′ primer, andgel-purified PCR product 32 or a vector that contains that PCR product;the resulting PCR product is gel purified and used in a second PCR withthe second 5′ PTD-4 primer and the 3′ primer. This PCR product is gelpurified and inserted into the pET100/D-TOPO® vector following themanufacturer's directions. For an Arg tag, a first PCR is carried outwith the first 5′ Arg primer, the 3′ primer, and gel-purified PCRproduct 32 or a vector that contains that PCR product; the resulting PCRproduct is gel purified and used in a second PCR with the second 5′ Argprimer and the 3′ primer. This PCR product is gel purified and insertedinto the pET100/D-TOPO® vector following the manufacturer's directions.For no protein transduction tag, a PCR is carried out with the 5′ primerfor no tag, the 3′ primer, and gel-purified PCR product 32 or a vectorthat contains that PCR product; the resulting PCR product is gelpurified and inserted into the pET100/D-TOPO® vector following themanufacturer's directions. The inserts in pET100/D-TOPO® are sequencedon both strands for sequence confirmation.

FIG. 81 illustrates PCR primers for producing a DNA sequence thatincludes the coding sequence from PCR product 33 fused to one of thefollowing protein transduction tags: TAT, PTD-4, an arginine-richsequence Arg, or no protein transduction tag. Glycine residues areincluded at the ends of the protein transduction tags to permit rotationor flexing of the resulting amino acid sequence at those points. For aTAT tag, a first PCR is carried out with the first 5′ TAT primer, the 3′primer, and gel-purified PCR product 33 or a vector that contains thatPCR product; the resulting PCR product is gel purified and used in asecond PCR with the second 5′ TAT primer and the 3′ primer. This PCRproduct is gel purified and inserted into the pET100/D-TOPO® vectorfollowing the manufacturer's directions. For a PTD-4 tag, a first PCR iscarried out with the first 5′ PTD-4 primer, the 3′ primer, andgel-purified PCR product 33 or a vector that contains that PCR product;the resulting PCR product is gel purified and used in a second PCR withthe second 5′ PTD-4 primer and the 3′ primer. This PCR product is gelpurified and inserted into the pET100/D-TOPO® vector following themanufacturer's directions. For an Arg tag, a first PCR is carried outwith the first 5′ Arg primer, the 3′ primer, and gel-purified PCRproduct 33 or a vector that contains that PCR product; the resulting PCRproduct is gel purified and used in a second PCR with the second 5′ Argprimer and the 3′ primer. This PCR product is gel purified and insertedinto the pET100/D-TOPO® vector following the manufacturer's directions.For no protein transduction tag, a PCR is carried out with the 5′ primerfor no tag, the 3′ primer, and gel-purified PCR product 33 or a vectorthat contains that PCR product; the resulting PCR product is gelpurified and inserted into the pET100/D-TOPO® vector following themanufacturer's directions. The inserts in pET100/D-TOPO® are sequencedon both strands for sequence confirmation.

FIG. 82 illustrates PCR primers for producing a DNA sequence thatincludes the coding sequence from PCR product 34 fused to one of thefollowing protein transduction tags: TAT, PTD-4, an arginine-richsequence Arg, or no protein transduction tag. Glycine residues areincluded at the ends of the protein transduction tags to permit rotationor flexing of the resulting amino acid sequence at those points. For aTAT tag, a first PCR is carried out with the first 5′ TAT primer, the 3′primer, and gel-purified PCR product 34 or a vector that contains thatPCR product; the resulting PCR product is gel purified and used in asecond PCR with the second 5′ TAT primer and the 3′ primer. This PCRproduct is gel purified and inserted into the pET100/D-TOPO® vectorfollowing the manufacturer's directions. For a PTD-4 tag, a first PCR iscarried out with the first 5′ PTD-4 primer, the 3′ primer, andgel-purified PCR product 34 or a vector that contains that PCR product;the resulting PCR product is gel purified and used in a second PCR withthe second 5′ PTD-4 primer and the 3′ primer. This PCR product is gelpurified and inserted into the pET100/D-TOPO® vector following themanufacturer's directions. For an Arg tag, a first PCR is carried outwith the first 5′ Arg primer, the 3′ primer, and gel-purified PCRproduct 34 or a vector that contains that PCR product; the resulting PCRproduct is gel purified and used in a second PCR with the second 5′ Argprimer and the 3′ primer. This PCR product is gel purified and insertedinto the pET100/D-TOPO® vector following the manufacturer's directions.For no protein transduction tag, a PCR is carried out with the 5′ primerfor no tag, the 3′ primer, and gel-purified PCR product 34 or a vectorthat contains that PCR product; the resulting PCR product is gelpurified and inserted into the pET100/D-TOPO® vector following themanufacturer's directions. The inserts in pET100/D-TOPO® are sequencedon both strands for sequence confirmation.

FIG. 83 illustrates PCR primers for producing a DNA sequence thatincludes the coding sequence from PCR product 35 fused to one of thefollowing protein transduction tags: TAT, PTD-4, an arginine-richsequence Arg, or no protein transduction tag. Glycine residues areincluded at the ends of the protein transduction tags to permit rotationor flexing of the resulting amino acid sequence at those points. For aTAT tag, a first PCR is carried out with the first 5′ TAT primer, the 3′primer, and gel-purified PCR product 35 or a vector that contains thatPCR product; the resulting PCR product is gel purified and used in asecond PCR with the second 5′ TAT primer and the 3′ primer. This PCRproduct is gel purified and inserted into the pET100/D-TOPO® vectorfollowing the manufacturer's directions. For a PTD-4 tag, a first PCR iscarried out with the first 5′ PTD-4 primer, the 3′ primer, andgel-purified PCR product 35 or a vector that contains that PCR product;the resulting PCR product is gel purified and used in a second PCR withthe second 5′ PTD-4 primer and the 3′ primer. This PCR product is gelpurified and inserted into the pET100/D-TOPO® vector following themanufacturer's directions. For an Arg tag, a first PCR is carried outwith the first 5′ Arg primer, the 3′ primer, and gel-purified PCRproduct 35 or a vector that contains that PCR product; the resulting PCRproduct is gel purified and used in a second PCR with the second 5′ Argprimer and the 3′ primer. This PCR product is gel purified and insertedinto the pET100/D-TOPO® vector following the manufacturer's directions.For no protein transduction tag, a PCR is carried out with the 5′ primerfor no tag, the 3′ primer, and gel-purified PCR product 35 or a vectorthat contains that PCR product; the resulting PCR product is gelpurified and inserted into the pET100/D-TOPO® vector following themanufacturer's directions. The inserts in pET100/D-TOPO® are sequencedon both strands for sequence confirmation.

FIG. 84 illustrates PCR primers for producing a DNA sequence thatincludes the coding sequence from PCR product 36 fused to one of thefollowing protein transduction tags: TAT, PTD-4, an arginine-richsequence Arg, or no protein transduction tag. Glycine residues areincluded at the ends of the protein transduction tags to permit rotationor flexing of the resulting amino acid sequence at those points. For aTAT tag, a first PCR is carried out with the first 5′ TAT primer, the 3′primer, and gel-purified PCR product 36 or a vector that contains thatPCR product; the resulting PCR product is gel purified and used in asecond PCR with the second 5′ TAT primer and the 3′ primer. This PCRproduct is gel purified and inserted into the pET100/D-TOPO® vectorfollowing the manufacturer's directions. For a PTD-4 tag, a first PCR iscarried out with the first 5′ PTD-4 primer, the 3′ primer, andgel-purified PCR product 36 or a vector that contains that PCR product;the resulting PCR product is gel purified and used in a second PCR withthe second 5′ PTD-4 primer and the 3′ primer. This PCR product is gelpurified and inserted into the pET100/D-TOPO® vector following themanufacturer's directions. For an Arg tag, a first PCR is carried outwith the first 5′ Arg primer, the 3′ primer, and gel-purified PCRproduct 36 or a vector that contains that PCR product; the resulting PCRproduct is gel purified and used in a second PCR with the second 5′ Argprimer and the 3′ primer. This PCR product is gel purified and insertedinto the pET100/D-TOPO® vector following the manufacturer's directions.For no protein transduction tag, a PCR is carried out with the 5′ primerfor no tag, the 3′ primer, and gel-purified PCR product 36 or a vectorthat contains that PCR product; the resulting PCR product is gelpurified and inserted into the pET100/D-TOPO® vector following themanufacturer's directions. The inserts in pET100/D-TOPO® are sequencedon both strands for sequence confirmation.

FIG. 85 illustrates PCR primers for producing a DNA sequence thatincludes the coding sequence from PCR product 37 fused to one of thefollowing protein transduction tags: TAT, PTD-4, an arginine-richsequence Arg, or no protein transduction tag. Glycine residues areincluded at the ends of the protein transduction tags to permit rotationor flexing of the resulting amino acid sequence at those points. For aTAT tag, a first PCR is carried out with the first 5′ TAT primer, the 3′primer, and gel-purified PCR product 37 or a vector that contains thatPCR product; the resulting PCR product is gel purified and used in asecond PCR with the second 5′ TAT primer and the 3′ primer. This PCRproduct is gel purified and inserted into the pET100/D-TOPO® vectorfollowing the manufacturer's directions. For a PTD-4 tag, a first PCR iscarried out with the first 5′ PTD-4 primer, the 3′ primer, andgel-purified PCR product 37 or a vector that contains that PCR product;the resulting PCR product is gel purified and used in a second PCR withthe second 5′ PTD-4 primer and the 3′ primer. This PCR product is gelpurified and inserted into the pET100/D-TOPO® vector following themanufacturer's directions. For an Arg tag, a first PCR is carried outwith the first 5′ Arg primer, the 3′ primer, and gel-purified PCRproduct 37 or a vector that contains that PCR product; the resulting PCRproduct is gel purified and used in a second PCR with the second 5′ Argprimer and the 3′ primer. This PCR product is gel purified and insertedinto the pET100/D-TOPO® vector following the manufacturer's directions.For no protein transduction tag, a PCR is carried out with the 5′ primerfor no tag, the 3′ primer, and gel-purified PCR product 37 or a vectorthat contains that PCR product; the resulting PCR product is gelpurified and inserted into the pET100/D-TOPO® vector following themanufacturer's directions. The inserts in pET100/D-TOPO® are sequencedon both strands for sequence confirmation.

FIG. 86 illustrates PCR primers for producing a DNA sequence thatincludes the coding sequence from PCR product 38 fused to one of thefollowing protein transduction tags: TAT, PTD-4, an arginine-richsequence Arg, or no protein transduction tag. Glycine residues areincluded at the ends of the protein transduction tags to permit rotationor flexing of the resulting amino acid sequence at those points. For aTAT tag, a first PCR is carried out with the first 5′ TAT primer, the 3′primer, and gel-purified PCR product 38 or a vector that contains thatPCR product; the resulting PCR product is gel purified and used in asecond PCR with the second 5′ TAT primer and the 3′ primer. This PCRproduct is gel purified and inserted into the pET100/D-TOPO® vectorfollowing the manufacturer's directions. For a PTD-4 tag, a first PCR iscarried out with the first 5′ PTD-4 primer, the 3′ primer, andgel-purified PCR product 38 or a vector that contains that PCR product;the resulting PCR product is gel purified and used in a second PCR withthe second 5′ PTD-4 primer and the 3′ primer. This PCR product is gelpurified and inserted into the pET100/D-TOPO® vector following themanufacturer's directions. For an Arg tag, a first PCR is carried outwith the first 5′ Arg primer, the 3′ primer, and gel-purified PCRproduct 38 or a vector that contains that PCR product; the resulting PCRproduct is gel purified and used in a second PCR with the second 5′ Argprimer and the 3′ primer. This PCR product is gel purified and insertedinto the pET100/D-TOPO® vector following the manufacturer's directions.For no protein transduction tag, a PCR is carried out with the 5′ primerfor no tag, the 3′ primer, and gel-purified PCR product 38 or a vectorthat contains that PCR product; the resulting PCR product is gelpurified and inserted into the pET100/D-TOPO® vector following themanufacturer's directions. The inserts in pET100/D-TOPO® are sequencedon both strands for sequence confirmation.

The relevant teachings of all the references, patents and patentapplications cited herein are incorporated herein by reference in theirentirety.

While this invention has been particularly described with references topreferred embodiments thereof, it will be understood by those skilled inthe art that various changes in form and details may be made thereinwithout departing from the scope of the invention encompassed by theappended claims.

1. A method of treating or preventing a pathogen infection in a cell,comprising administering to said cell chimeric molecules having at leastone pathogen-detection domain and at least one effector domain, saidpathogen-detection domain being one not naturally bound to said effectordomain, whereby in the presence of a pathogen in the cell, said chimericmolecules bind to the pathogen and activate said effector domain,thereby treating or preventing the pathogen infection in said cell.
 2. Amethod of treating or preventing a pathogen infection in a cell,comprising administering to said cell chimeric molecules having at leastone pathogen-induced product-detection domain and at least one effectordomain, said pathogen-induced product-detection domain being one notnaturally bound to said effector domain, whereby in the presence of apathogen-induced product in said cell, the chimeric molecules bind tothe pathogen-induced product and activate said effector domain, therebytreating or preventing the pathogen infection in said cell.
 3. A methodof treating or preventing the spread of a pathogen infection in anorganism, comprising administering to said organism chimeric moleculeshaving at least one pathogen-detection domain and at least one effectordomain, said pathogen-detection domain being one not naturally bound tosaid effector domain, whereby in the presence of a pathogen in a cell ofsaid organism, said chimeric molecules bind to the pathogen and activatesaid effector domain, thereby treating or preventing the spread of saidpathogen infection in said organism.
 4. A method of treating orpreventing the spread of a pathogen infection in an organism, comprisingadministering to said organism chimeric molecules having at least onepathogen-induced product-detection domain and at least one effectordomain, said pathogen-induced product-detection domain being one notnaturally bound to said effector domain, whereby in the presence of apathogen-induced product in a cell of said organism, said chimericmolecules bind to the pathogen-induced product and activate saideffector domain, thereby treating or preventing the spread of saidpathogen infection in said organism.
 5. A method of treating orpreventing a pathogen infection in a cell, comprising administering tosaid cell an agent, wherein said agent comprises at least onepathogen-interacting molecular structure and at least oneeffector-mediating molecular structure, said agent being one that isnon-naturally-occurring in said cell, whereby in the presence of apathogen in said cell, the agent binds to the pathogen and activates theeffector-mediating molecular structure, thereby treating or preventingthe pathogen infection in said cell.
 6. A method of treating orpreventing a pathogen infection in a cell, comprising administering tosaid cell an agent, wherein said agent comprises at least onepathogen-induced product-interacting molecular structure and at leastone effector-mediating molecular structure, said agent being one that isnon-naturally-occurring in a cell, whereby in the presence of apathogen-induced product in said cell, the agent binds to thepathogen-induced product and activates the effector-mediating molecularstructure, thereby treating or preventing the pathogen infection in saidcell.
 7. A method of treating or preventing the spread of a pathogeninfection in an organism, comprising administering to said organism anagent, wherein said agent comprises at least one pathogen-interactingmolecular structure and at least one effector-mediating molecularstructure, said agent being one that is non-naturally-occurring in acell, whereby in the presence of a pathogen in a cell of said organism,the agent binds to the pathogen and activates the effector-mediatingmolecular structure, thereby treating or preventing the spread of saidpathogen infection in said organism.
 8. A method of treating orpreventing the spread of a pathogen infection in an organism, comprisingadministering to said organism an agent, wherein said agent comprises atleast one pathogen-induced product-interacting molecular structure andat least one effector-mediating molecular structure, said agent beingone that is non-naturally-occurring in a cell, whereby in the presenceof a pathogen-induced product in a cell of said organism, the agentbinds to the pathogen-induced product and activates theeffector-mediating molecular structure, thereby treating or preventingthe spread of said pathogen infection in said organism.
 9. A method oftreating or preventing a pathogen infection in a cell, comprisingadministering to said cell individual components of a chimeric molecule,wherein said components of said chimeric molecule assemble together toform the chimeric molecule, said assembled chimeric molecule having atleast one pathogen-detection domain and at least one effector domain,said pathogen-detection domain being one not naturally assembled withsaid effector domain, whereby in the presence of a pathogen in saidcell, the chimeric molecule binds to the pathogen and activates saideffector domain, thereby treating or preventing a pathogen infection insaid cell.
 10. A method of treating or preventing a pathogen infectionin a cell, comprising administering to said cell individual componentsof a chimeric molecule, wherein said components of said chimericmolecule assemble together to form the chimeric molecule, said assembledchimeric molecule having at least one pathogen-induced product-detectiondomain and at least one effector domain, said pathogen-inducedproduct-detection domain being one not naturally assembled with saideffector domain, whereby in the presence of a pathogen-induced productin said cell, the chimeric molecule binds to the pathogen-inducedproduct and activates said effector domain, thereby treating orpreventing a pathogen infection in said cell.
 11. A method of treatingor preventing the spread of a pathogen infection in an organism,comprising administering to said organism individual components of achimeric molecule, wherein said components of said chimeric moleculeassemble together to form the chimeric molecule, said assembled chimericmolecule having at least one pathogen-detection domain and at least oneeffector domain, said pathogen-detection domain being one not naturallyassembled with said effector domain, whereby in the presence of apathogen in a cell of said organism, said chimeric molecule binds to thepathogen and activates said effector domain, thereby treating orpreventing the spread of a pathogen infection in said organism.
 12. Amethod of treating or preventing the spread of a pathogen infection inan organism, comprising administering to said organism individualcomponents of a chimeric molecule, wherein said components of saidchimeric molecule assemble together to form the chimeric molecule, saidassembled chimeric molecule having at least one pathogen-inducedproduct-detection domain and at least one effector domain, saidpathogen-induced product-detection domain being one not naturallyassembled with said effector domain, whereby in the presence of apathogen-induced product in a cell of said organism, said chimericmolecule binds to the pathogen-induced product and activates saideffector domain, thereby treating or preventing the spread of a pathogeninfection in said organism.
 13. A chimeric molecule having at least onepathogen-detection domain and at least one effector domain, saidchimeric molecule being one that is non-naturally-occurring in a cell.14. A chimeric molecule having at least one pathogen-inducedproduct-detection domain and at least one effector domain, said chimericmolecule being one that is non-naturally-occurring in a cell.
 15. Anagent having at least one pathogen-interacting molecular structure andat least one effector-mediating molecular structure, said agent beingone that is non-naturally-occurring in a cell.
 16. An agent having atleast one pathogen-induced product-interacting molecular structure andat least one effector-mediating molecular structure, said agent beingone that is non-naturally-occurring in a cell.
 17. An assay for thedetection of a pathogen infection in a cell, comprising the steps of: a)culturing said cell in a suitable cell culture medium; b) administeringto said cell a chimeric molecule having at least one pathogen-detectiondomain and at least one effector domain, said chimeric molecule beingone that is non-naturally-occurring in a cell, whereby in the presenceof a pathogen in said cell, said chimeric molecule binds to saidpathogen and activates said effector domain; and c) determining thepresence or absence of effector domain activation; whereby activation ofsaid effector domain indicates the presence of a pathogen infection insaid cell.
 18. An assay for the detection of a pathogen infection in anorganism, comprising the steps of: a) obtaining a cell from saidorganism; b) culturing said cell in a suitable cell culture medium; c)administering to said cell a chimeric molecule having at least onepathogen-detection domain and at least one effector domain, saidchimeric molecule being one that is non-naturally-occurring in a cell,whereby in the presence of a pathogen in said cell, said chimericmolecule binds to said pathogen and activates said effector domain; andd) determining the presence or absence of effector domain activation;whereby activation of said effector domain indicates the presence of apathogen infection in said cell in said organism.
 19. An assay for thedetection of a pathogen infection in an organism, comprising the stepsof: a) obtaining a sample from said organism; b) adding said sample toan uninfected cell; c) culturing said cell in a suitable cell culturemedium; d) administering to said cell a chimeric molecule having atleast one pathogen-detection domain and at least one effector domain,said chimeric molecule being one that is non-naturally-occurring in acell, whereby in the presence of a pathogen in said cell, said chimericmolecule binds to said pathogen and activates said effector domain; ande) determining the presence or absence of effector domain activation;whereby activation of said effector domain indicates the presence of apathogen infection in the sample obtained from said organism.
 20. Anassay for the detection of a pathogen infection in a cell, comprising:a) culturing said cell in a suitable cell culture medium; b)administering to said cell an agent having at least onepathogen-interacting molecular structure and at least oneeffector-mediating molecular structure, said agent being one that isnon-naturally-occurring in said cell, whereby in the presence of apathogen in said cell, said agent binds to said pathogen and activatessaid effector-mediating molecular structure; and c) determining thepresence or absence of effector-mediating molecular structureactivation; whereby activation of said effector-mediating molecularstructure indicates the presence of a pathogen infection in said cell.21. An assay for the detection of a pathogen infection in an organism,comprising the steps of: a) obtaining a cell from said organism; b)culturing said cell in a suitable cell culture medium; c) administeringto said cell an agent having at least one pathogen-interacting molecularstructure and at least one effector-mediating molecular structure, saidagent being one that is non-naturally-occurring in said cell, whereby inthe presence of a pathogen in said cell, said agent binds to saidpathogen and activates said effector-mediating molecular structure; andd) determining the presence or absence of effector-mediating molecularstructure activation; whereby activation of said effector-mediatingmolecular structure indicates the presence of a pathogen infection insaid organism.
 22. An assay for the detection of a pathogen infection ina cell, comprising: a) culturing said cell in a suitable cell culturemedium; b) administering to said cell a chimeric molecule having atleast one pathogen-induced product-detection domain and at least oneeffector domain, said chimeric molecule being one that isnon-naturally-occurring in a cell, whereby in the presence of apathogen-induced product in said cell, said chimeric molecule binds tosaid pathogen-induced product and activates said effector domain; and c)determining the presence or absence of effector domain activation;whereby activation of said effector domain indicates the presence of apathogen infection in said cell.
 23. An assay for the detection of apathogen infection in an organism, comprising: a) obtaining a cell fromsaid organism; b) culturing said cell in a suitable cell culture medium;c) administering to said cell a chimeric molecule having at least onepathogen-induced product-detection domain and at least one effectordomain, said chimeric molecule being one that is non-naturally-occurringin a cell, whereby in the presence of a pathogen-induced product in saidcell, said chimeric molecule binds to said pathogen-induced product andactivates said effector domain; and d) determining the presence orabsence of effector domain activation; whereby activation of saideffector domain indicates the presence of a pathogen infection in saidcell in said organism.
 24. An assay for the detection of a pathogeninfection in an organism, comprising: a) obtaining a sample from saidorganism; b) adding said sample to an uninfected cell; c) culturing saidcell in a suitable cell culture medium; d) administering to said cell achimeric molecule having at least one pathogen-induced product-detectiondomain and at least one effector domain, said chimeric molecule beingone that is non-naturally-occurring in a cell, whereby in the presenceof a pathogen-induced product in said cell, said chimeric molecule bindsto said pathogen-induced product and activates said effector domain; ande) determining the presence or absence of effector domain activation;whereby activation of said effector domain indicates the presence of apathogen infection in the sample obtained from said organism.
 25. Anassay for the detection of a pathogen infection in a cell, comprising:a) culturing said cell in a suitable cell culture medium; b)administering to said cell an agent having at least one pathogen-inducedproduct-interacting molecular structure and at least oneeffector-mediating molecular structure, said agent being one that isnon-naturally-occurring in said cell, whereby in the presence of apathogen-induced product in said cell, said agent binds to saidpathogen-induced product and activates said effector-mediating molecularstructure; and c) determining the presence or absence ofeffector-mediating molecular structure activation; whereby activation ofsaid effector-mediating molecular structure indicates the presence of apathogen infection in said cell.
 26. An assay for the detection of apathogen infection in an organism, comprising: a) obtaining a cell fromsaid organism; b) culturing said cell in a suitable cell culture medium;c) administering to said cell an agent having at least onepathogen-induced product-interacting molecular structure and at leastone effector-mediating molecular structure, said agent being one that isnon-naturally-occurring in said cell, whereby in the presence of apathogen-induced product in said cell, said agent binds to saidpathogen-induced product and activates said effector-mediating molecularstructure; and d) determining the presence or absence ofeffector-mediating molecular structure activation; whereby activation ofsaid effector-mediating molecular structure indicates the presence of apathogen infection in said organism.
 27. A chimeric molecule having atleast one pathogen-detection domain and at least one effector domain,said chimeric molecule being one that is non-naturally-occurring in acell, wherein said pathogen-detection domain is a double-stranded RNAbinding domain isolated from protein kinase R and said effector domainis an apoptosis mediator domain isolated from FLICE Activated DeathDomain (FADD), whereby in the presence of double-stranded RNA, chimericmolecules bind to the double-stranded RNA and activate said apoptosismediator domain.
 28. An agent having at least one double-strandedRNA-interacting molecular structure isolated from protein kinase R andat least one apoptosis-effector mediating molecular structure isolatedfrom FLICE Activated Death Domain (FADD), said agent being one that isnon-naturally-occurring in a cell, whereby in the presence ofdouble-stranded RNA, said agent binds to the double-stranded RNA andactivates said apoptosis-effector mediating molecular structure.